Design of multi-binding-site inhibitors, ligand efficiency, and consensus screening of avian influenza H5N1 wild-type neuraminidase and of the oseltamivir-resistant H274Y variant

Journal of Chemical Information and Modeling

Volumn 48, Issue 10, 2008, Pages 2074-2080

  García Sosa, Alfonso T ^a   Siid, Sulev ^a   Maran, Uko ^a  

^a UNIVERSITY OF TARTU   (Estonia)

Author keywords

[No Author keywords available]

Indexed keywords

BINDING ENERGY; EFFICIENCY; LIGANDS; VIRUSES;

AVIAN INFLUENZA A; CONSENSUS SCORING; DOCKING METHODS; EFFICIENCY INDEX; INHIBITOR DESIGN; OPEN CONFORMATION; PHARMACOKINETIC PROPERTIES; VIRTUAL SCREENING;

BINDING SITES;

ANTIVIRUS AGENT; ENZYME INHIBITOR; LIGAND; OSELTAMIVIR; PEPTIDE LIBRARY; SIALIDASE;

ANTIVIRAL RESISTANCE; ARTICLE; BINDING SITE; CHEMICAL STRUCTURE; COMPUTER PROGRAM; DIMERIZATION; DRUG ANTAGONISM; DRUG DESIGN; DRUG SCREENING; ENZYMOLOGY; GENETICS; INFLUENZA VIRUS A H5N1; PROTEIN CONFORMATION;

ANTIVIRAL AGENTS; BINDING SITES; DIMERIZATION; DRUG DESIGN; DRUG EVALUATION, PRECLINICAL; DRUG RESISTANCE, VIRAL; ENZYME INHIBITORS; INFLUENZA A VIRUS, H5N1 SUBTYPE; LIGANDS; MODELS, MOLECULAR; NEURAMINIDASE; OSELTAMIVIR; PEPTIDE LIBRARY; PROTEIN CONFORMATION; SOFTWARE;

EID: 56449084239     PISSN: 15499596     EISSN: 1549960X     Source Type: Journal    
DOI: 10.1021/ci800242z     Document Type: Article

References (36)

1. World Health Organization. Cumulative Number of Confirmed Human Cases of Avian Influenza A/(H5N1) Reported to WHO, 18 Mar 2008, 2008.
2. World Health Organization. Influenza A (H5N1) in Hong Kong Special Administrative Region of China, 19 Feb 2003, 2003.
3. Kim, C. U.; Lew, W.; Williams, M. A.; Liu, H. T.; Zhang, L. J.; Swaminathan, S.; Bischofberger, N.; Chen, M. S.; Mendel, D. B.; Tai, C. Y.; Laver, W. G.; Stevens, R. C. Influenza neuraminidase inhibitors possessing a novel hydrophobic interaction in the enzyme active site: Design, synthesis, and structural analysis of carbocyclic sialic acid analogues with potent anti-influenza activity. J. Am. Chem. Soc. 1997, 119, 681-690.
4. von Itzstein, M.; Wu, W. Y.; Kok, G. B.; Pegg, M. S.; Dyason, J. C.; Jun, B.; Van Phan, T.; Smythe, M. L.; White, H. F.; Oliver, S. W.; Colma, P. M.; Varghese, J. N.; Ryan, D. M.; Woods, J. M.; Bethell, R. C.; Hotham, V. J.; Cameron, J. M.; Penn, C. R. Rational design of potent sialidase-based inhibitors of influenza-virus replication. Nature 1993, 363, 418-423.
5. Gubareva, L. V.; Kaiser, L.; Matrosovich, M. N.; Soo-Hoo, Y.; Hayden, F. G. Selection of influenza virus mutants in experimentally infected volunteers treated with oseltamivir. J. Infect. Dis. 2001, 183, 523-531.
6. European Union. European Center for Disease Prevention and Control. Resistance to oseltamivir (Tamiflu) found in some European Influenza samples, http://ecdc.europa.eu (accessed Apr 16, 2008).
7. Collins, P. J.; Haire, L. F.; Lin, Y. P.; Liu, J.; Russell, R. J.; Walker, P. A.; Skehel, J. J.; Martin, S. R.; Hay, A. J.; Gamblin, S. J. Crystal structures of oseltamivir-resistant influenza virus neuraminidase mutants. Nature 2008, 453, 1258-1261.
8. Russell, R. J.; Haire, L. F.; Stevens, D. J.; Collins, P. J.; Lin, Y. P.; Blackburn, G. M.; Hay, A. J.; Gamblin, S. J.; Skehel, J. J. The structure of H5N1 avian influenza neuraminidase suggests new opportunities for drug design. Nature 2006, 443 (7107), 45-49.
9. Amaro, R. E.; Minh, D. D. L.; Cheng, L. S.; Lindstrom, W. M.; Olson, A. J.; Lin, J.-H.; McCammon, J. A. Remarkable loop flexibility in avian influenza NI and its implications for antiviral drug design. J. Am. Chem. Soc. 2007, 129, 7764-7765.
10. Kuntz, I. D.; Chen, K.; Sharp, K. A.; Kollman, P. A. The maximal affinity of ligands. Proc. Natl. Acad Sci. U.S.A. 1999, 96, 9997-10002.
11. Hopkins, A. L.; Groom, C. R.; Alex, A. Ligand efficiency: A useful metric for lead system. Drug Discovery Today 2004, 9, 430-431.
12. Abad-Zapatero, C.; Metz, J. T. Ligand efficiency indices as guideposts for drug discovery. Drug Discovery Today 2005, 10, 464-469.
13. Hetényi, C.; Maran, U.; García-Sosa, A. T.; Karelson, M. Structure-based calculation of drug efficiency indices. Bioinformatics 2007, 23, 2678-2685.
14. Wells, J. A.; McClendon, C. L. Reaching for high-hanging fruit in drug discovery at protein-protein interfaces. Nature 2007, 450, 1001-1009.
15. Lipinski, C. A.; Lombardo, F.; Dominy, B. W.; Feeney, P. J. Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv. Drug Delivery Rev. 1997, 23, 3-25.
16. Ghose, A. K.; Vellarkad, V. N.; Wendoloski, J. J. A knowledge-based approach in designing combinatorial or medicinal chemistry libraries for drug discovery. 1. A qualitative and quantitative characterization of known drug databases. J. Comb. Chem. 1998, 1, 55-68.
17. University of Alberta, Canada, DrugBank.www.drugbank.ca (accessed Mar 16, 2008).
18. Wishart, D. S.; Knox, C.; Guo, A. C.; Shrivastava, S.; Hassanali, M.; Stothard, P.; Chang, Z.; Woolsey, J. DrugBank: A knowledgebase for drugs, drug actions and drug targets. Nucleic Acids Res. 2006, 34, D668-D672.
19. National Cancer Institute/National Institutes of Health USA. DTP-Diversity Set Information, http://dtp.nci.nih.gov/branches/dscb/ diversity_explanation.html (accessed Mar 16, 2008).
20. Irwin, J. J.; Shoichet, B. K. ZINC-A free database of commercially available compounds for virtual screening. J. Chem. Inf. Model. 2005, 45, 177-182.
21. Glide, version.4.5; Schrödinger, LLC: New York, 2007.
22. Morris, G. M.; Goodsell, D. S.; Halliday, R. S.; Huey, R.; Hart, W. E.; Belew, R. K.; Olson, A. J. Automated docking using a Lamarckian genetic algorithm and an empirical binding free energy function. J. Comput. Chem. 1998, 19, 1639-1662.
23. LigPrep, version.2.1; Schrödinger, LLC: New York, 2007.
24. Chemomentum consortium. Chemomentum. http://www.chemomentum.org. (accessed Jan 15, 2008).
25. Maran, U.; Sild, S.; Mazzatorta, P.; Casalegno, M.; Benfenati, E.; Romberg, M. Grid computing for the estimation of toxicity: acute toxicity on fathead minnow (Pimephales prometas). In Distributed, High-Performance and Grid Computing in Computational Biology; Dubitsky, W., Schuster, A., Sloot, P. M. A., Schroeder, M., Romberg, M., Eds.; Springer-Verlag: Berlin Heidelberg, 2007.
26. Schuller, B.; Demuth, B.; Mix, H.; Rasch, K.; Romberg, M.; Sild, S.; Maran, U.; Bała, P.; del Grosso, E.; Casalegno, M.; Piclin, N.; Pintore, M.; Sudholt, W.; Baldridge K. K., Chemomentum-UNICORE 6 based infrastructure for complex applications in science and technology. In Theoretical Computer Science and General Issues; Bougé, L., Forsell, M., Larsson Träff, J., Streit, A., Ziegler, W., Alexander, M., Childs, S., Eds. Springer-Verlag: Berlin, 2008.
27. Distributed Systems and Grid Computing, Juelich Supercomputing Centre, Institute for Advanced Simulation, Research Centre Juelich, Germany. UNICORE-Distributed computing and data resources. http://www.unicore.eu (accessed Jan 15, 2008).
28. Almond, J.; Snelling, D. UNICORE: Uniform access to supercomputing as an element of electronic commerce. Future Gener. Comput. Syst. 1999, 613, 539-548.
29. Open Babel, http://openbabel.org (accessed 15 Mar, 2007).
30. Maestro, version 8.0; Schrödinger, LLC: New York, 2007.
31. Wang, R.; Gao, Y.; Lai, L. Calculating partition coefficient by atomadditive method. Perspect. Drug Discov. 2000, 19, 47-66.
32. Marvin, version 4.8.1; ChemAxon: Budapest, Hungary, 2007; http:// www.chemaxon.com.
33. Virtual Screening Workflow; Schrödinger, LLC: New York, 2007.
34. Hetényi, C.; van der Spoel, D. Efficient docking of peptides to proteins without prior knowledge of the binding site. Protein Sci. 2002, 11, 1729-2737.
35. Hetényi, C.; van der Spoel, D. Blind docking of drug-sized compounds to proteins with up to a thousand residues. FEBS Lett. 2006, 580, 1447-1450.
36. Cheng, L. S.; Amaro, R. E.; Xu, D.; Li, W. W.; Arzberger, P. W.; McCammon, A. Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase. J. Med. Chem. 2008, 51 (13), 3878-3894.