1f8d Citations

Analysis of inhibitor binding in influenza virus neuraminidase.

Protein Sci 10 689-96 (2001)
Related entries: 1f8b, 1f8c, 1f8e

Cited: 47 times
EuropePMC logo PMID: 11274459

Abstract

2,3-didehydro-2-deoxy-N:-acetylneuraminic acid (DANA) is a transition state analog inhibitor of influenza virus neuraminidase (NA). Replacement of the hydroxyl at the C9 position in DANA and 4-amino-DANA with an amine group, with the intention of taking advantage of an increased electrostatic interaction with a conserved acidic group in the active site to improve inhibitor binding, significantly reduces the inhibitor activity of both compounds. The three-dimensional X-ray structure of the complexes of these ligands and NA was obtained to 1.4 A resolution and showed that both ligands bind isosterically to DANA. Analysis of the geometry of the ammonium at the C4 position indicates that Glu119 may be neutral when these ligands bind. A computational analysis of the binding energies indicates that the substitution is successful in increasing the energy of interaction; however, the gains that are made are not sufficient to overcome the energy that is required to desolvate that part of the ligand that comes in contact with the protein.

Reviews - 1f8d mentioned but not cited (1)

  1. Function and 3D structure of the N-glycans on glycoproteins. Nagae M, Yamaguchi Y. Int J Mol Sci 13 8398-8429 (2012)

Articles - 1f8d mentioned but not cited (7)

  1. Analysis of inhibitor binding in influenza virus neuraminidase. Smith BJ, Colman PM, Von Itzstein M, Danylec B, Varghese JN. Protein Sci. 10 689-696 (2001)
  2. Dynameomics: a consensus view of the protein unfolding/folding transition state ensemble across a diverse set of protein folds. Jonsson AL, Scott KA, Daggett V. Biophys. J. 97 2958-2966 (2009)
  3. Crystal structure of a new benzoic acid inhibitor of influenza neuraminidase bound with a new tilt induced by overpacking subsite C6. Venkatramani L, Johnson ES, Kolavi G, Air GM, Brouillette WJ, Mooers BH. BMC Struct. Biol. 12 7 (2012)
  4. Customizable de novo design strategies for DOCK: Application to HIVgp41 and other therapeutic targets. Allen WJ, Fochtman BC, Balius TE, Rizzo RC. J Comput Chem 38 2641-2663 (2017)
  5. A Diverse Benchmark Based on 3D Matched Molecular Pairs for Validating Scoring Functions. Kalinowsky L, Weber J, Balasupramaniam S, Baumann K, Proschak E. ACS Omega 3 5704-5714 (2018)
  6. Molecular-level simulation of pandemic influenza glycoproteins. Amaro RE, Li WW. Methods Mol. Biol. 819 575-594 (2012)
  7. Prediction of the Inhibition of Influenza Virus Neuraminidase Various Strains by Means of a Generalized Model Constructed Using the Data on the Position of Known Ligands. Mikurova AV, Rybina AV, Skvortsov VS. Biochem Mosc Suppl B Biomed Chem 15 166-170 (2021)


Reviews citing this publication (4)

  1. Antivirals Targeting the Neuraminidase. Gubareva L, Mohan T. Cold Spring Harb Perspect Med 12 a038455 (2022)
  2. Influenza Neuraminidase Inhibitors: Synthetic Approaches, Derivatives and Biological Activity. Laborda P, Wang SY, Voglmeir J. Molecules 21 (2016)
  3. The clinical significance of sialoderiveratives in the search for novel means of antipathogen therapy. Werling D. Equine Vet. J. 38 390-392 (2006)
  4. Zwitterionic structures: from physicochemical properties toward computer-aided drug designs. Yang Z, Li Q, Yang G. Future Med Chem 8 2245-2262 (2016)

Articles citing this publication (35)

  1. Importance of neuraminidase active-site residues to the neuraminidase inhibitor resistance of influenza viruses. Yen HL, Hoffmann E, Taylor G, Scholtissek C, Monto AS, Webster RG, Govorkova EA. J. Virol. 80 8787-8795 (2006)
  2. DOCK 6: Impact of new features and current docking performance. Allen WJ, Balius TE, Mukherjee S, Brozell SR, Moustakas DT, Lang PT, Case DA, Kuntz ID, Rizzo RC. J Comput Chem 36 1132-1156 (2015)
  3. Thermodynamic basis for promiscuity and selectivity in protein-protein interactions: PDZ domains, a case study. Basdevant N, Weinstein H, Ceruso M. J. Am. Chem. Soc. 128 12766-12777 (2006)
  4. Study of drug resistance of chicken influenza A virus (H5N1) from homology-modeled 3D structures of neuraminidases. Wang SQ, Du QS, Chou KC. Biochem. Biophys. Res. Commun. 354 634-640 (2007)
  5. Multiple field three dimensional quantitative structure-activity relationship (MF-3D-QSAR). Du QS, Huang RB, Wei YT, Du LQ, Chou KC. J Comput Chem 29 211-219 (2008)
  6. Insights from modeling the 3D structure of H5N1 influenza virus neuraminidase and its binding interactions with ligands. Wei DQ, Du QS, Sun H, Chou KC. Biochem. Biophys. Res. Commun. 344 1048-1055 (2006)
  7. Analogue inhibitors by modifying oseltamivir based on the crystal neuraminidase structure for treating drug-resistant H5N1 virus. Du QS, Wang SQ, Chou KC. Biochem. Biophys. Res. Commun. 362 525-531 (2007)
  8. Sensitivity of molecular docking to induced fit effects in influenza virus neuraminidase. Birch L, Murray CW, Hartshorn MJ, Tickle IJ, Verdonk ML. J. Comput. Aided Mol. Des. 16 855-869 (2002)
  9. Investigation of atomic level patterns in protein--small ligand interactions. Chen K, Kurgan L. PLoS ONE 4 e4473 (2009)
  10. Is it possible to increase hit rates in structure-based virtual screening by pharmacophore filtering? An investigation of the advantages and pitfalls of post-filtering. Muthas D, Sabnis YA, Lundborg M, Karlén A. J. Mol. Graph. Model. 26 1237-1251 (2008)
  11. Molecular dynamics and free energy analysis of neuraminidase-ligand interactions. Bonnet P, Bryce RA. Protein Sci. 13 946-957 (2004)
  12. On the lower susceptibility of oseltamivir to influenza neuraminidase subtype N1 than those in N2 and N9. Aruksakunwong O, Malaisree M, Decha P, Sompornpisut P, Parasuk V, Pianwanit S, Hannongbua S. Biophys. J. 92 798-807 (2007)
  13. A Balance between Inhibitor Binding and Substrate Processing Confers Influenza Drug Resistance. Jiang L, Liu P, Bank C, Renzette N, Prachanronarong K, Yilmaz LS, Caffrey DR, Zeldovich KB, Schiffer CA, Kowalik TF, Jensen JD, Finberg RW, Wang JP, Bolon DNA. J. Mol. Biol. 428 538-553 (2016)
  14. Binding of a natural anthocyanin inhibitor to influenza neuraminidase by mass spectrometry. Swaminathan K, Dyason JC, Maggioni A, von Itzstein M, Downard KM. Anal Bioanal Chem 405 6563-6572 (2013)
  15. Development of recombinant protein-based influenza vaccine. Expression and affinity purification of H1N1 influenza virus neuraminidase. Dalakouras T, Smith BJ, Platis D, Cox MM, Labrou NE. J Chromatogr A 1136 48-56 (2006)
  16. Scoring binding affinity of multiple ligands using implicit solvent and a single molecular dynamics trajectory: application to influenza neuraminidase. Bonnet P, Bryce RA. J. Mol. Graph. Model. 24 147-156 (2005)
  17. Conformational analysis and design of cross-strand disulfides in antiparallel β-sheets. Indu S, Kochat V, Thakurela S, Ramakrishnan C, Varadarajan R. Proteins 79 244-260 (2011)
  18. The conformational analysis and proton transfer of neuraminidase inhibitors: a theoretical study. Yang Z, Yang G, Zu Y, Fu Y, Zhou L. Phys Chem Chem Phys 11 10035-10041 (2009)
  19. A Gibbs free energy correlation for automated docking of carbohydrates. Hill AD, Reilly PJ. J Comput Chem 29 1131-1141 (2008)
  20. Exploring the mechanism of zanamivir resistance in a neuraminidase mutant: a molecular dynamics study. Han N, Liu X, Mu Y. PLoS ONE 7 e44057 (2012)
  21. Getting it right: modeling of pH, solvent and "nearly" everything else in virtual screening of biological targets. Kellogg GE, Fornabaio M, Spyrakis F, Lodola A, Cozzini P, Mozzarelli A, Abraham DJ. J. Mol. Graph. Model. 22 479-486 (2004)
  22. Mutation effects of neuraminidases and their docking with ligands: a molecular dynamics and free energy calculation study. Yang Z, Yang G, Zhou L. J. Comput. Aided Mol. Des. 27 935-950 (2013)
  23. Unsaturated N-acetyl- D-glucosaminuronic acid glycosides as inhibitors of influenza virus sialidase. Mann MC, Islam T, Dyason JC, Florio P, Trower CJ, Thomson RJ, von Itzstein M. Glycoconj J 23 127-133 (2006)
  24. Combining docking, scoring and molecular field analyses to probe influenza neuraminidase-ligand interactions. Abu Hammad AM, Afifi FU, Taha MO. J. Mol. Graph. Model. 26 443-456 (2007)
  25. Influenza virus neuraminidase contributes to the dextran sulfate-dependent suppressive replication of some influenza A virus strains. Yamada H, Moriishi E, Haredy AM, Takenaka N, Mori Y, Yamanishi K, Okamoto S. Antiviral Res. 96 344-352 (2012)
  26. Computer-based de novo designs of tripeptides as novel neuraminidase inhibitors. Yang Z, Yang G, Zu Y, Fu Y, Zhou L. Int J Mol Sci 11 4932-4951 (2010)
  27. Integration of neuraminidase inhibitor assay into a single-step operation using a combinable poly(dimethylsiloxane) capillary sensor. Ishimoto T, Jigawa K, Henares TG, Endo T, Hisamoto H. Analyst 138 3158-3162 (2013)
  28. Potential New H1N1 Neuraminidase Inhibitors from Ferulic Acid and Vanillin: Molecular Modelling, Synthesis and in Vitro Assay. Hariono M, Abdullah N, Damodaran KV, Kamarulzaman EE, Mohamed N, Hassan SS, Shamsuddin S, Wahab HA. Sci Rep 6 38692 (2016)
  29. Exploring Strong Interactions in Proteins with Quantum Chemistry and Examples of Their Applications in Drug Design. Xie NZ, Du QS, Li JX, Huang RB. PLoS ONE 10 e0137113 (2015)
  30. Homology modeling of human transketolase: description of critical sites useful for drug design and study of the cofactor binding mode. Obiol-Pardo C, Rubio-Martinez J. J. Mol. Graph. Model. 27 723-734 (2009)
  31. Progress in structure-based drug design against influenza A virus. Du QS, Wei H, Huang RB, Chou KC. Expert Opin Drug Discov 6 619-631 (2011)
  32. Exploring the inhibition of the soluble lytic transglycosylase Cj0843c of Campylobacter jejuni via targeting different sites with different scaffolds. Kumar V, Boorman J, Greenlee WJ, Zeng X, Lin J, van den Akker F. Protein Sci 32 e4683 (2023)
  33. Characterization of the malaria parasite protein PfTip, a novel invasion-related protein. Liu X, Huang Y, Liang J, Wang J, Shen Y, Li Y, Zhao Y. Mol Med Rep 13 3303-3310 (2016)
  34. Optimisation of Neuraminidase Expression for Use in Drug Discovery by Using HEK293-6E Cells. Campbell AC, Tanner JJ, Krause KL. Viruses 13 1893 (2021)
  35. The making of a potent L-lactate transport inhibitor. Bosshart PD, Kalbermatter D, Bonetti S, Fotiadis D. Commun Chem 4 128 (2021)