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Journal articles on the topic 'Influenza A Virus, NMR'

Author: Grafiati

Published: 9 March 2023

Last updated: 10 March 2023

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1

Sabesan, Subramaniam, Jens O. Duus, Susana Neira, Peter Domaille, Soerge Kelm, James C. Paulson, and Klaus Bock. "Cluster sialoside inhibitors for influenza virus: synthesis, NMR, and biological studies." Journal of the American Chemical Society 114, no. 22 (October 1992): 8363–75. http://dx.doi.org/10.1021/ja00048a004.

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2

Jadhav, P., M. Borkar, K. Malbari, M. Joshi, and M. Kanyalkar. "DESIGN, SYNTHESIS AND MOLECULAR MECHANISM OF FEW NEURAMINIDASE INHIBITORS IN TREATMENT OF H1N1 BY NMR TECHNIQUES." INDIAN DRUGS 56, no. 02 (February 26, 2019): 7–15. http://dx.doi.org/10.53879/id.56.02.11584.

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Considering the issue of resistance to anti-influenza drugs, there is a need for discovery of new antiviral drugs. In view of this, flavones and their synthetic precursors i.e. chalcones were designed as inhibitors of influenza virus - H1N1 neuraminidase enzyme using structure-based drug design. Based on the best docking scores, some chalcone and flavone derivatives were synthesized and characterized by IR and proton NMR. Few of them were selected for 31P NMR studies, in order to probe the molecular mechanism of their antiviral action. Reasonably good correlation between docking scores and 31P NMR results were observed. As antiviral drugs are known to show membrane stabilizing effect on host cell, 31P NMR data for methoxy chalcone showed stabilization effect on model membrane pointing towards good antiviral activity which remained unaffected even after its cyclization to flavone. These derivatives can be explored further to provide a future therapeutic option for the treatment and prophylaxis of H1N1 viral infections.

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3

Cheong, H. "Structure of influenza virus panhandle RNA studied by NMR spectroscopy and molecular modeling." Nucleic Acids Research 27, no. 5 (March 1, 1999): 1392–97. http://dx.doi.org/10.1093/nar/27.5.1392.

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4

SABESAN, S., J. OE DUUS, S. NEIRA, P. DOMAILLE, S. KELM, J. C. PAULSON, and K. BOCK. "ChemInform Abstract: Cluster Sialoside Inhibitors for Influenza Virus: Synthesis, NMR, and Biological Studies." ChemInform 24, no. 7 (August 20, 2010): no. http://dx.doi.org/10.1002/chin.199307273.

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5

Chang, S., J. Zhang, X. Liao, X. Zhu, D. Wang, J. Zhu, T. Feng, et al. "Influenza Virus Database (IVDB): an integrated information resource and analysis platform for influenza virus research." Nucleic Acids Research 35, Database (January 3, 2007): D376—D380. http://dx.doi.org/10.1093/nar/gkl779.

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6

Toraya, S., A. Naito, S. Tuzi, and H. Saito. "pH-dependent Fusogenic Mechanism of Influenza Virus Hemagglutinin2(1-27)Using Solid-state NMR." Seibutsu Butsuri 41, supplement (2001): S132. http://dx.doi.org/10.2142/biophys.41.s132_3.

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7

Cheong, H. "Secondary structure of the panhandle RNA of influenza virus A studied by NMR spectroscopy." Nucleic Acids Research 24, no. 21 (November 1, 1996): 4197–201. http://dx.doi.org/10.1093/nar/24.21.4197.

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8

Elkins, Matthew R., Jonathan K. Williams, Martin D. Gelenter, Peng Dai, Byungsu Kwon, Ivan V. Sergeyev, Bradley L. Pentelute, and Mei Hong. "Cholesterol-binding site of the influenza M2 protein in lipid bilayers from solid-state NMR." Proceedings of the National Academy of Sciences 114, no. 49 (November 20, 2017): 12946–51. http://dx.doi.org/10.1073/pnas.1715127114.

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The influenza M2 protein not only forms a proton channel but also mediates membrane scission in a cholesterol-dependent manner to cause virus budding and release. The atomic interaction of cholesterol with M2, as with most eukaryotic membrane proteins, has long been elusive. We have now determined the cholesterol-binding site of the M2 protein in phospholipid bilayers using solid-state NMR spectroscopy. Chain-fluorinated cholesterol was used to measure cholesterol proximity to M2 while sterol-deuterated cholesterol was used to measure bound-cholesterol orientation in lipid bilayers. Carbon–fluorine distance measurements show that at a cholesterol concentration of 17 mol%, two cholesterol molecules bind each M2 tetramer. Cholesterol binds the C-terminal transmembrane (TM) residues, near an amphipathic helix, without requiring a cholesterol recognition sequence motif. Deuterium NMR spectra indicate that bound cholesterol is approximately parallel to the bilayer normal, with the rough face of the sterol rings apposed to methyl-rich TM residues. The distance- and orientation-restrained cholesterol-binding site structure shows that cholesterol is stabilized by hydrophobic interactions with the TM helix and polar and aromatic interactions with neighboring amphipathic helices. At the 1:2 binding stoichiometry, lipid 31P spectra show an isotropic peak indicative of high membrane curvature. This M2–cholesterol complex structure, together with previously observed M2 localization at phase boundaries, suggests that cholesterol mediates M2 clustering to the neck of the budding virus to cause the necessary curvature for membrane scission. The solid-state NMR approach developed here is generally applicable for elucidating the structural basis of cholesterol’s effects on membrane protein function.

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9

Zhang, Yun, Brian D. Aevermann, Tavis K. Anderson, David F. Burke, Gwenaelle Dauphin, Zhiping Gu, Sherry He, et al. "Influenza Research Database: An integrated bioinformatics resource for influenza virus research." Nucleic Acids Research 45, no. D1 (September 26, 2016): D466—D474. http://dx.doi.org/10.1093/nar/gkw857.

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10

Liao, Yu-Chieh, Chin-Yu Ko, Ming-Hsin Tsai, Min-Shi Lee, and Chao A. Hsiung. "ATIVS: analytical tool for influenza virus surveillance." Nucleic Acids Research 37, suppl_2 (May 8, 2009): W643—W646. http://dx.doi.org/10.1093/nar/gkp321.

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11

Bao, Jie, Xin-Ya Xu, Xiao-Yong Zhang, and Shu-Hua Qi. "A New Macrolide from a Marine-derived Fungus Aspergillus sp." Natural Product Communications 8, no. 8 (August 2013): 1934578X1300800. http://dx.doi.org/10.1177/1934578x1300800825.

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A new 16-membered macrolide named aspergillide D (1), along with six known compounds, including two polyketones (2–3) and four alkaloids (4–7), were isolated from the culture broth of a marine-derived fungus Aspergillus sp. SCSGAF 0076. The structure of 1 was elucidated on the basis of NMR and mass spectra. Compound 5 showed an obvious inhibitory effect on influenza virus strains H1N1 and H3N2.

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12

Zhou, Guoliang, Xiaomin Zhang, Mudassir Shah, Qian Che, Guojian Zhang, Qianqun Gu, Tianjiao Zhu, and Dehai Li. "Polyhydroxy p-Terphenyls from a Mangrove Endophytic Fungus Aspergillus candidus LDJ-5." Marine Drugs 19, no. 2 (February 2, 2021): 82. http://dx.doi.org/10.3390/md19020082.

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Six undescribed polyhydroxy p-terphenyls, namely asperterphenyllins A–F, were isolated from an endophytic fungus Aspergillus candidus LDJ-5. Their structures were determined by NMR and MS data. Differing from the previously reported p-terphenyls, asperterphenyllin A represents the first p-terphenyl dimer connected by a C-C bond. Asperterphenyllin A displayed anti-influenza virus A (H1N1) activity and protein tyrosine phosphatase 1B (PTP1B) inhibitory activity with IC50 values of 53 μM and 21 μM, respectively. The anti-influenza virus A (H1N1) activity and protein tyrosine phosphatase 1B (PTP1B) inhibitory activity of p-terphenyls are reported for the first time. Asperterphenyllin G exhibited cytotoxicity against nine cell lines with IC50 values ranging from 0.4 to 1.7 μM. Asperterphenyllin C showed antimicrobial activity against Proteus species with a MIC value of 19 μg/mL.

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13

Almatrrouk, Shaihana, Iram Saba, Suhair Abozaid, Ahmed A. Al-Qahtani, and Mohammed N. Al-Ahdal. "Virus sensing receptors in cellular infectivity of influenza A virus." Journal of Infection in Developing Countries 15, no. 01 (January 31, 2021): 1–8. http://dx.doi.org/10.3855/jidc.13258.

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An innate immune response is essential to mobilize protective immunity upon the infection of respiratory epithelial cells with influenza A virus (IAV). The response is classified as early (nonspecific effectors), local systematic (effector cells recruitment) and late (antigen to lymphoid organ transport, naive B and T cells recognition, effector cells clonal expansion and differentiation). Virus particles are detected by the host cells as non-self by various sensors that are present on the cell surface, endosomes and cytosol. These sensors are collectively termed as pattern recognition receptors (PRRs). The PRRs distinguish unique molecular signatures known as pathogen-associated molecular pattern, which are present either on the cell surface or within intracellular compartments. PRRs have been classified into five major groups: C-Type Lectin Receptor (CLR), Toll-like receptor (TLR), Nod-like receptor (NLR), Retinoic acid-inducible gene-I-like receptor (RLR), which play a role in innate immunity to IAV infection, and the pyrin and hematopoietic interferon-inducible nuclear (PYHIN) domain protein. Here, we discuss the role of PRRs in cellular infectivity of IAV and highlight the recent progress.

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14

Turan, K. "Nuclear MxA proteins form a complex with influenza virus NP and inhibit the transcription of the engineered influenza virus genome." Nucleic Acids Research 32, no. 2 (January 21, 2004): 643–52. http://dx.doi.org/10.1093/nar/gkh192.

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15

Milner, J. Justin, Jue Wang, Patricia A. Sheridan, Tim Ebbels, Melinda A. Beck, and Jasmina Saric. "1H NMR-Based Profiling Reveals Differential Immune-Metabolic Networks during Influenza Virus Infection in Obese Mice." PLoS ONE 9, no. 5 (May 20, 2014): e97238. http://dx.doi.org/10.1371/journal.pone.0097238.

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16

Haselhorst, Thomas, Jean-Michel Garcia, Tasneem Islam, Jimmy C C. Lai, Faith J Rose, John M Nicholls, J. S. Malik Peiris, and Mark von Itzstein. "Avian Influenza H5-Containing Virus-Like Particles (VLPs): Host-Cell Receptor Specificity by STD NMR Spectroscopy." Angewandte Chemie 120, no. 10 (February 22, 2008): 1936–38. http://dx.doi.org/10.1002/ange.200704872.

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17

Haselhorst, Thomas, Jean-Michel Garcia, Tasneem Islam, Jimmy C C. Lai, Faith J Rose, John M Nicholls, J. S. Malik Peiris, and Mark von Itzstein. "Avian Influenza H5-Containing Virus-Like Particles (VLPs): Host-Cell Receptor Specificity by STD NMR Spectroscopy." Angewandte Chemie International Edition 47, no. 10 (February 22, 2008): 1910–12. http://dx.doi.org/10.1002/anie.200704872.

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18

Han, Meng-Yi, Tian-Ao Xie, Jia-Xin Li, Hui-Jin Chen, Xiao-Hui Yang, and Xu-Guang Guo. "Evaluation of Lateral-Flow Assay for Rapid Detection of Influenza Virus." BioMed Research International 2020 (September 8, 2020): 1–16. http://dx.doi.org/10.1155/2020/3969868.

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Background. Influenza virus mainly causes acute respiratory infections in humans. However, the diagnosis of influenza is not accurate based on clinical evidence, as the symptoms of flu are similar to other respiratory virus. The lateral-flow assay is a rapid method to detect influenza virus. But the effectiveness of the technique in detecting flu viruses is unclear. Hence, a meta-analysis would be performed to evaluate the accuracy of LFA in detecting influenza virus. Methods. Relevant literature was searched out in PubMed, Embase, Web of Science, and Cochrane Library databases with the keywords “lateral flow assay” and “flu virus”. By Meta-DiSc software, pooled sensitivity, pooled specificity, positive likelihood ratio (PLR), negative likelihood ratio (NLR), diagnostic odds ratio (DOR), summary receiver operating characteristic curve (SROC), and area under the curve (AUC) can be calculated. Results. This meta-analysis contains 13 studies and 24 data. The pooled sensitivity and specificity of the influenza virus detected by LFA were 0.84 (95% CI: 0.82-0.86) and 0.97 (95% CI: 0.97-0.98), respectively. The pooled values of PLR, NLR, DOR, and SROC were 32.68 (17.16-62.24), 0.17 (0.13-0.24), 334.07 (144.27-773.53), and 0.9877. No publication bias was found. Conclusions. LFA exhibited high sensitivity and specificity in diagnosing influenza virus. It is a valuable alternative method which can diagnose influenza virus quickly. However, more evidence is required to confirm whether LFA is comparable to traditional methods for detecting the virus.

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19

Li, Jiao, Yujia Wang, Xiaomeng Hao, Shasha Li, Jia Jia, Yan Guan, Zonggen Peng, et al. "Broad-Spectrum Antiviral Natural Products from the Marine-Derived Penicillium sp. IMB17-046." Molecules 24, no. 15 (August 2, 2019): 2821. http://dx.doi.org/10.3390/molecules24152821.

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A new pyrazine derivative, trypilepyrazinol (1), a new α-pyrone polyketide, (+)-neocitreoviridin (2), and a new ergostane analogue, 3β-hydroxyergosta-8,14,24(28)-trien-7-one (3), were isolated and characterized along with five known compounds from the marine-derived fungus Penicillium sp. IMB17-046. The structures of these new compounds were determined using spectroscopic data analyses (HRESIMS, 1D- and 2D-NMR), X-ray crystallography analysis, and TDDFT ECD calculation. Compounds 1 and 3 exhibited broad-spectrum antiviral activities against different types of viruses, including human immunodeficiency virus (HIV), hepatitis C virus (HCV), and influenza A virus (IAV), with IC50 values ranging from 0.5 to 7.7 μM. Compounds 1 and 2 showed antibacterial activities against Helicobacter pylori, a causative pathogen of various gastric diseases, with minimum inhibitory concentration (MIC) values of 1–16 μg/mL.

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20

Zhou, Zhe, Jed C. Macosko, Donald W. Hughes, Brian G. Sayer, John Hawes, and Richard M. Epand. "15N NMR Study of the Ionization Properties of the Influenza Virus Fusion Peptide in Zwitterionic Phospholipid Dispersions." Biophysical Journal 78, no. 5 (May 2000): 2418–25. http://dx.doi.org/10.1016/s0006-3495(00)76785-3.

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21

Liao, Shu Yu, Keith J. Fritzsching, and Mei Hong. "Conformational analysis of the full-length M2 protein of the influenza A virus using solid-state NMR." Protein Science 22, no. 11 (October 7, 2013): 1623–38. http://dx.doi.org/10.1002/pro.2368.

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22

Bao, Y., P. Bolotov, D. Dernovoy, B. Kiryutin, and T. Tatusova. "FLAN: a web server for influenza virus genome annotation." Nucleic Acids Research 35, Web Server (May 8, 2007): W280—W284. http://dx.doi.org/10.1093/nar/gkm354.

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23

Lu, G., T. Rowley, R. Garten, and R. O. Donis. "FluGenome: a web tool for genotyping influenza A virus." Nucleic Acids Research 35, Web Server (May 8, 2007): W275—W279. http://dx.doi.org/10.1093/nar/gkm365.

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24

Dong, Tao. "CD8+ cytotoxic T lymphocytes in human influenza virus infection." National Science Review 2, no. 3 (June 29, 2015): 264–65. http://dx.doi.org/10.1093/nsr/nwv033.

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25

Ha, Thi Kim Quy, Ba Wool Lee, Ngoc Hieu Nguyen, Hyo Moon Cho, Thamizhiniyan Venkatesan, Thi Phuong Doan, Eunhee Kim, and Won Keun Oh. "Antiviral Activities of Compounds Isolated from Pinus densiflora (Pine Tree) against the Influenza A Virus." Biomolecules 10, no. 5 (May 4, 2020): 711. http://dx.doi.org/10.3390/biom10050711.

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Pinus densiflora was screened in an ongoing project to discover anti-influenza candidates from natural products. An extensive phytochemical investigation provided 26 compounds, including two new megastigmane glycosides (1 and 2), 21 diterpenoids (3–23), and three flavonoids (24–26). The chemical structures were elucidated by a series of chemical reactions, including modified Mosher’s analysis and various spectroscopic measurements such as LC/MS and 1D- and 2D-NMR. The anti-influenza A activities of all isolates were screened by cytopathic effect (CPE) inhibition assays and neuraminidase (NA) inhibition assays. Ten candidates were selected, and detailed mechanistic studies were performed by various assays, such as Western blot, immunofluorescence, real-time PCR and flow cytometry. Compound 5 exerted its antiviral activity not by direct neutralizing virion surface proteins, such as HA, but by inhibiting the expression of viral mRNA. In contrast, compound 24 showed NA inhibitory activity in a noncompetitive manner with little effect on viral mRNA expression. Interestingly, both compounds 5 and 24 were shown to inhibit nitric oxide (NO) production and inducible nitric oxide synthase (iNOS) expression in a dose-dependent manner. Taken together, these results provide not only the chemical profiling of P. densiflora but also anti-influenza A candidates.

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26

Luo, Wenbin, Rajeswari Mani, and Mei Hong. "Side-Chain Conformation of the M2 Transmembrane Peptide Proton Channel of Influenza A Virus from19F Solid-State NMR." Journal of Physical Chemistry B 111, no. 36 (September 2007): 10825–32. http://dx.doi.org/10.1021/jp073823k.

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27

Tian, Changlin, Kurt Tobler, Robert A. Lamb, Lawrence H. Pinto, and T. A. Cross. "Expression and Initial Structural Insights from Solid-State NMR of the M2 Proton Channel from Influenza A Virus†." Biochemistry 41, no. 37 (September 2002): 11294–300. http://dx.doi.org/10.1021/bi025695q.

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28

Wakefield, Larrissa, and George G. Brownlee. "RNA-binding properties of influenza A virus matrix protein M1." Nucleic Acids Research 17, no. 21 (1989): 8569–80. http://dx.doi.org/10.1093/nar/17.21.8569.

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29

Ichinohe, Takeshi, Heung Kyu Lee, Yasunori Ogura, Richard Flavell, and Akiko Iwasaki. "Inflammasome recognition of influenza virus is essential for adaptive immune responses." Journal of Experimental Medicine 206, no. 1 (January 12, 2009): 79–87. http://dx.doi.org/10.1084/jem.20081667.

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Influenza virus infection is recognized by the innate immune system through Toll like receptor (TLR) 7 and retinoic acid inducible gene I. These two recognition pathways lead to the activation of type I interferons and resistance to infection. In addition, TLR signals are required for the CD4 T cell and IgG2a, but not cytotoxic T lymphocyte, responses to influenza virus infection. In contrast, the role of NOD-like receptors (NLRs) in viral recognition and induction of adaptive immunity to influenza virus is unknown. We demonstrate that respiratory infection with influenza virus results in the activation of NLR inflammasomes in the lung. Although NLRP3 was required for inflammasome activation in certain cell types, CD4 and CD8 T cell responses, as well as mucosal IgA secretion and systemic IgG responses, required ASC and caspase-1 but not NLRP3. Consequently, ASC, caspase-1, and IL-1R, but not NLRP3, were required for protective immunity against flu challenge. Furthermore, we show that caspase-1 inflammasome activation in the hematopoietic, but not stromal, compartment was required to induce protective antiviral immunity. These results demonstrate that in addition to the TLR pathways, ASC inflammasomes play a central role in adaptive immunity to influenza virus.

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30

Dhakal, Puspa, and Bishnu Pd. Pokhrel. "Seasonal Variation and COVID-19 Pandemic in Nepal." Nepal Medical Journal 3, no. 2 (December 31, 2020): 77–80. http://dx.doi.org/10.37080/nmj.137.

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The World Health Organization has declared the novel coronavirus (SARS-CoV-2) Covid-19 as a pandemic as it has spread globally. Understanding severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) global dispersal pattern, it is important to know the environmental parameters within which the virus survives. There is adequate evidence in epidemiological and biological aspects to prove human beings are prone to viral pathogens such as Middle East respiratory syndrome coronavirus, respiratory syncytial virus, and influenza virus in cold weather. Apart from the influence of seasonality, other factors that might impact the rate of virus spread includes the effectiveness of infection control practices, individual behavior and immunity, and emergency preparedness levels of countries. This viewpoint highlights the potential influence of weather conditions, seasons, and non-climatological factors on the geographical spread of cases of COVID-19 across the globe.

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31

Lee, Woonghee, Ronnie O. Frederick, Marco Tonelli, and Ann C. Palmenberg. "Solution NMR Determination of the CDHR3 Rhinovirus-C Binding Domain, EC1." Viruses 13, no. 2 (January 22, 2021): 159. http://dx.doi.org/10.3390/v13020159.

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Cadherin Related Family Member 3 (CDHR3) is the identified and required cellular receptor for all virus isolates in the rhinovirus-C species (RV-C). Cryo-EM determinations recently resolved the atomic structure of RV-C15a, and subsequently, a complex of this virus bound to CDHR3 extracellular domain 1 (EC1), the N-terminal portion of this receptor responsible for virus interactions. The EC1 binds to a hypervariable sequence footprint on the virus surface, near the 3-fold axis of icosahedral symmetry. The key contacts involve discontinuous residues from 3 viral proteins, VP1, VP2 and VP3. That single cryo-EM EC1 structure, however, could not resolve whether the virus-receptor interface was structurally adaptable to accommodate multiple virus sequences. We now report the solution NMR determination of CDHR3 EC1, showing that this protein, in fact, is mostly inflexible, particularly in the virus-binding face. The new, higher resolution dataset identifies 3 cis-Pro residues in important loop regions, where they can influence both rigidity and overall protein conformation. The data also provide clarification about the residues involved in essential calcium ion binding, and a potential CDHR3 surface groove feature that may be involved in native protein interactions with cellular partners.

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Hornick, Emma, Balaji Banoth, Ann Miller, Zeb Ralph Zacharias, Nidhi Jain, Mary E. Wilson, Katherine Gibson-Corley, et al. "Nlrp12 mediates adverse neutrophil recruitment during influenza virus infection." Journal of Immunology 200, no. 1_Supplement (May 1, 2018): 60.3. http://dx.doi.org/10.4049/jimmunol.200.supp.60.3.

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Abstract Exaggerated inflammatory responses during influenza A virus (IAV) infection are typically associated with severe disease. Neutrophils are among the immune cells that can drive this excessive and detrimental inflammation. In moderation, however, neutrophils are necessary for optimal viral control. In this study, we explore the role of the nucleotide-binding domain leucinerich repeat containing receptor (NLR) family member Nlrp12 in modulating neutrophilic responses during lethal IAV infection. Nlrp12−/− mice are protected from lethality during IAV infection and show decreased vascular permeability, fewer pulmonary neutrophils, and a reduction in levels of neutrophil chemoattractant CXCL1 in their lungs compared to wild-type (WT) mice. Nlrp12−/− neutrophils and dendritic cells (DCs) within the IAV-infected lungs produce less CXCL1 than their WT counterparts. Decreased CXCL1 production by Nlrp12−/− cells was not due to a difference in CXCL1 protein stability, but instead to a decrease in Cxcl1 mRNA stability. Together, these data demonstrate a previously unappreciated role for Nlrp12 in exacerbating the pathogenesis of IAV infection through the regulation of CXCL1 mediated neutrophilic responses.

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33

Luo, Wenbin, Sarah D. Cady, and Mei Hong. "Immobilization of the Influenza A M2 Transmembrane Peptide in Virus Envelope−Mimetic Lipid Membranes: A Solid-State NMR Investigation." Biochemistry 48, no. 27 (July 14, 2009): 6361–68. http://dx.doi.org/10.1021/bi900716s.

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Lee, Charlie Wah Heng, Chee Wee Koh, Yang Sun Chan, Pauline Poh Kim Aw, Kuan Hon Loh, Bing Ling Han, Pei Ling Thien, et al. "Large-scale evolutionary surveillance of the 2009 H1N1 influenza A virus using resequencing arrays." Nucleic Acids Research 38, no. 9 (February 25, 2010): e111-e111. http://dx.doi.org/10.1093/nar/gkq089.

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ABSTRACT In April 2009, a new influenza A (H1N1 2009) virus emerged that rapidly spread around the world. While current variants of this virus have caused widespread disease, particularly in vulnerable groups, there remains the possibility that future variants may cause increased virulence, drug resistance or vaccine escape. Early detection of these virus variants may offer the chance for increased containment and potentially prevention of the virus spread. We have developed and field-tested a resequencing kit that is capable of interrogating all eight segments of the 2009 influenza A(H1N1) virus genome and its variants, with added focus on critical regions such as drug-binding sites, structural components and mutation hotspots. The accompanying base-calling software (EvolSTAR) introduces novel methods that utilize neighbourhood hybridization intensity profiles and substitution bias of probes on the microarray for mutation confirmation and recovery of ambiguous base queries. Our results demonstrate that EvolSTAR is highly accurate and has a much improved call rate. The high throughput and short turn-around time from sample to sequence and analysis results (30 h for 24 samples) makes this kit an efficient large-scale evolutionary biosurveillance tool.

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35

Fournier, Emilie, Vincent Moules, Boris Essere, Jean-Christophe Paillart, Jean-Daniel Sirbat, Catherine Isel, Annie Cavalier, et al. "A supramolecular assembly formed by influenza A virus genomic RNA segments." Nucleic Acids Research 40, no. 5 (November 9, 2011): 2197–209. http://dx.doi.org/10.1093/nar/gkr985.

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36

Torreira, E., G. Schoehn, Y. Fernandez, N. Jorba, R. W. H. Ruigrok, S. Cusack, J. Ortin, and O. Llorca. "Three-dimensional model for the isolated recombinant influenza virus polymerase heterotrimer." Nucleic Acids Research 35, no. 11 (May 7, 2007): 3774–83. http://dx.doi.org/10.1093/nar/gkm336.

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37

Wang, W., Z. Q. Cui, H. Han, Z. P. Zhang, H. P. Wei, Y. F. Zhou, Z. Chen, and X. E. Zhang. "Imaging and characterizing influenza A virus mRNA transport in living cells." Nucleic Acids Research 36, no. 15 (July 24, 2008): 4913–28. http://dx.doi.org/10.1093/nar/gkn475.

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38

Krasnov, Victor P., Vera V. Musiyak, Galina L. Levit, Dmitry A. Gruzdev, Valeriya L. Andronova, Georgii A. Galegov, Iana R. Orshanskaya, Ekaterina O. Sinegubova, Vladimir V. Zarubaev, and Valery N. Charushin. "Synthesis of Pyrimidine Conjugates with 4-(6-Amino-hexanoyl)-7,8-difluoro-3,4-dihydro-3-methyl-2H-[1,4]benzoxazine and Evaluation of Their Antiviral Activity." Molecules 27, no. 13 (June 30, 2022): 4236. http://dx.doi.org/10.3390/molecules27134236.

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A series of pyrimidine conjugates containing a fragment of racemic 7,8-difluoro-3,4-dihydro-3-methyl-2H-[1,4]benzoxazine and its (S)-enantiomer attached via a 6-aminohexanoyl fragment were synthesized by the reaction of nucleophilic substitution of chlorine in various chloropyrimidines. The structures of the synthesized compounds were confirmed by 1H, 19F, and 13C NMR spectral data. Enantiomeric purity of optically active derivatives was confirmed by chiral HPLC. Antiviral evaluation of the synthesized compounds has shown that the replacement of purine with a pyrimidine fragment leads to a decrease in the anti-herpesvirus activity compared to the lead compound, purine conjugate. The studied compounds did not exhibit significant activity against influenza A (H1N1) virus.

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39

Chiba-Kamoshida, K., N. Nemoto, and H. Nakanishi. "Analysis of an interaction between fusion peptide of hemagglutinin on the surface of influenza virus and SDS micelle by NMR method." Seibutsu Butsuri 40, supplement (2000): S31. http://dx.doi.org/10.2142/biophys.40.s31_2.

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40

Kang, Hui-Hui, Huai-Bin Zhang, Mei-Jia Zhong, Li-Ying Ma, De-Sheng Liu, Wei-Zhong Liu, and Hong Ren. "Potential Antiviral Xanthones from a Coastal Saline Soil Fungus Aspergillus iizukae." Marine Drugs 16, no. 11 (November 15, 2018): 449. http://dx.doi.org/10.3390/md16110449.

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Five new (1–5) and two known xanthones (6 and 7), one of the latter (6) obtained for the first time as a natural product, together with three known anthraquinones, questin, penipurdin A, and questinol, were isolated from the coastal saline soil-derived Aspergillus iizukae by application of an OSMAC (one strain many compounds) approach. Their structures were determined by interpretation of nuclear magnetic resonance (NMR) and high-resolution electrospray ionization mass spectroscopy (HRESIMS) data, as well as comparison of these data with those of related known compounds. Antiviral activity of xanthones 1−7 was evaluated through the cytopathic effect (CPE) inhibition assay, and compound 2 exhibited distinctly strong activity towards influenza virus (H1N1), herpes simplex virus types 1 (HSV-1) and 2 (HSV-2) with IC50 values of 44.6, 21.4, and 76.7 μM, respectively, which indicated that it was worth to further investigate it as a potential lead compound. The preliminary structure-activity relationship of the xanthones is discussed.

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Witter, Raiker, Farhod Nozirov, Ulrich Sternberg, Timothy A. Cross, Anne S. Ulrich, and Riqiang Fu. "Solid-State19F NMR Spectroscopy Reveals That Trp41Participates in the Gating Mechanism of the M2 Proton Channel of Influenza A Virus." Journal of the American Chemical Society 130, no. 3 (January 2008): 918–24. http://dx.doi.org/10.1021/ja0754305.

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Aramini, James M., Keith Hamilton, Li-Chung Ma, G. V. T. Swapna, Paul G. Leonard, John E. Ladbury, Robert M. Krug, and Gaetano T. Montelione. "19F NMR Reveals Multiple Conformations at the Dimer Interface of the Nonstructural Protein 1 Effector Domain from Influenza A Virus." Structure 22, no. 4 (April 2014): 515–25. http://dx.doi.org/10.1016/j.str.2014.01.010.

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Williams, Jonathan K., Daniel Tietze, Myungwoon Lee, Jun Wang, and Mei Hong. "Solid-State NMR Investigation of the Conformation, Proton Conduction, and Hydration of the Influenza B Virus M2 Transmembrane Proton Channel." Journal of the American Chemical Society 138, no. 26 (June 23, 2016): 8143–55. http://dx.doi.org/10.1021/jacs.6b03142.

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44

Huang, Ri-Bo, Qi-Shi Du, Cheng-Hua Wang, and Kuo-Chen Chou. "An in-depth analysis of the biological functional studies based on the NMR M2 channel structure of influenza A virus." Biochemical and Biophysical Research Communications 377, no. 4 (December 2008): 1243–47. http://dx.doi.org/10.1016/j.bbrc.2008.10.148.

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Sakudo, Akikazu, Koichi Baba, and Kazuyoshi Ikuta. "Discrimination of influenza virus-infected nasal fluids by Vis-NIR spectroscopy." Clinica Chimica Acta 414 (December 2012): 130–34. http://dx.doi.org/10.1016/j.cca.2012.08.022.

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Gog, Julia R., Emmanuel Dos Santos Afonso, Rosa M. Dalton, India Leclercq, Laurence Tiley, Debra Elton, Johann C. von Kirchbach, Nadia Naffakh, Nicolas Escriou, and Paul Digard. "Codon conservation in the influenza A virus genome defines RNA packaging signals." Nucleic Acids Research 35, no. 6 (March 1, 2007): 1897–907. http://dx.doi.org/10.1093/nar/gkm087.

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47

Shimizu, Kiyoshi, Hiroshi Handa, Susumu Nakada, and Kyosuke Nagata. "Regulation of influenza virus RNA polymerase activity by cellular and viral factors." Nucleic Acids Research 22, no. 23 (1994): 5047–53. http://dx.doi.org/10.1093/nar/22.23.5047.

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48

Yao, Hongwei, Michelle W. Lee, Alan J. Waring, Gerard C. L. Wong, and Mei Hong. "Viral fusion protein transmembrane domain adopts β-strand structure to facilitate membrane topological changes for virus–cell fusion." Proceedings of the National Academy of Sciences 112, no. 35 (August 17, 2015): 10926–31. http://dx.doi.org/10.1073/pnas.1501430112.

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The C-terminal transmembrane domain (TMD) of viral fusion proteins such as HIV gp41 and influenza hemagglutinin (HA) is traditionally viewed as a passive α-helical anchor of the protein to the virus envelope during its merger with the cell membrane. The conformation, dynamics, and lipid interaction of these fusion protein TMDs have so far eluded high-resolution structure characterization because of their highly hydrophobic nature. Using magic-angle-spinning solid-state NMR spectroscopy, we show that the TMD of the parainfluenza virus 5 (PIV5) fusion protein adopts lipid-dependent conformations and interactions with the membrane and water. In phosphatidylcholine (PC) and phosphatidylglycerol (PG) membranes, the TMD is predominantly α-helical, but in phosphatidylethanolamine (PE) membranes, the TMD changes significantly to the β-strand conformation. Measured order parameters indicate that the strand segments are immobilized and thus oligomerized. 31P NMR spectra and small-angle X-ray scattering (SAXS) data show that this β-strand–rich conformation converts the PE membrane to a bicontinuous cubic phase, which is rich in negative Gaussian curvature that is characteristic of hemifusion intermediates and fusion pores. 1H-31P 2D correlation spectra and 2H spectra show that the PE membrane with or without the TMD is much less hydrated than PC and PG membranes, suggesting that the TMD works with the natural dehydration tendency of PE to facilitate membrane merger. These results suggest a new viral-fusion model in which the TMD actively promotes membrane topological changes during fusion using the β-strand as the fusogenic conformation.

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Karupiah, Gunasegaran, Jian-He Chen, Surendran Mahalingam, Carl F. Nathan, and John D. MacMicking. "Rapid Interferon γ–dependent Clearance of Influenza A Virus and Protection from Consolidating Pneumonitis in Nitric Oxide Synthase 2–deficient Mice." Journal of Experimental Medicine 188, no. 8 (October 19, 1998): 1541–46. http://dx.doi.org/10.1084/jem.188.8.1541.

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Viral infection often activates the interferon (IFN)-γ–inducible gene, nitric oxide synthase 2 (NOS2). Expression of NOS2 can limit viral growth but may also suppress the immune system and damage tissue. This study assessed each of these effects in genetically deficient NOS2−/− mice after infection with influenza A, a virus against which IFN-γ has no known activity. At inocula sufficient to cause consolidating pneumonitis and death in wild-type control mice, NOS2−/− hosts survived with little histopathologic evidence of pneumonitis. Moreover, they cleared influenza A virus from their lungs by an IFN-γ–dependent mechanism that was not evident in wild-type mice. Even when the IFN-γ–mediated antiviral activity was blocked in NOS2−/− mice with anti–IFN-γ mAb, such mice failed to succumb to disease. Further evidence that this protection was independent of viral load was provided by treating NOS2+/+ mice with the NOS inhibitor, Nω-methyl-l-arginine (l-NMA). l-NMA prevented mortality without affecting viral growth. Thus, host NOS2 seems to contribute more significantly to the development of influenza pneumonitis in mice than the cytopathic effects of viral replication. Although NOS2 mediates some antiviral effects of IFN-γ, during influenza infection it can suppress another IFN-γ–dependent antiviral mechanism. This mechanism was observed only in the complete absence of NOS2 activity and appeared sufficient to control influenza A virus growth in the absence of changes in cytotoxic T lymphocyte activity.

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Ko, Keebeom, Seong-Hwan Kim, Subin Park, Hwa Seung Han, Jae Kyun Lee, Jin Wook Cha, Sunghoon Hwang, et al. "Discovery and Photoisomerization of New Pyrrolosesquiterpenoids Glaciapyrroles D and E, from Deep-Sea Sediment Streptomyces sp." Marine Drugs 20, no. 5 (April 22, 2022): 281. http://dx.doi.org/10.3390/md20050281.

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Two new pyrrolosesquiterpenes, glaciapyrroles D (1) and E (2) were discovered along with the previously reported glaciapyrrole A (3) from Streptomyces sp. GGS53 strain isolated from deep-sea sediment. This study elucidated the planar structures of 1 and 2 using nuclear magnetic resonance (NMR), mass spectrometry (MS), ultraviolet (UV), and infrared (IR) spectroscopic data. The absolute configurations of the glaciapyrroles were determined by Mosher’s method, circular dichroism spectroscopy, and X-ray crystallography. Under 366 nm UV irradiation, the glaciapyrroles were systematically converted to the corresponding photoglaciapyrroles (4–6) via photoisomerization, resulting in the diversification of the glaciapyrrole family compounds. The transformation of the glaciapyrrole Z to E isomers occurred in a 1:1 ratio, based on virtual validation of the photoisomerization of these olefinic compounds by 1H-NMR spectroscopy and liquid chromatography/mass spectrometry (LC/MS) analysis. Finally, when encapsulated in poly(lactic-co-glycolic acid) nanoparticles, glaciapyrrole E and photoglaciapyrrole E displayed significant inhibitory activity against influenza A virus. This is the first report of antiviral effects from glaciapyrrole family compounds, whose biological functions have only been subjected to limited studies so far.

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