Structure based design towards the identification of novel binding sites and inhibitors for the chikungunya virus envelope proteins

Journal of Molecular Graphics and Modelling

Volumn 44, Issue , 2013, Pages 241-252

  Rashad, Adel A ^a   Keller, Paul A ^a  

^a UNIVERSITY OF WOLLONGONG   (Australia)

Author keywords

Alphaviruses; Chikungunya virus; Envelope proteins; Virtual screening

Indexed keywords

BINS; CELL MEMBRANES; PROTEINS; VIRUSES;

ALPHAVIRUSES; CHIKUNGUNYA; ENVELOPE PROTEINS; MEDICINAL CHEMISTRY; POTENTIAL BINDING; STRUCTURE-BASED DESIGNS; VIRAL ENVELOPE PROTEINS; VIRTUAL SCREENING;

BINDING SITES;

CHIKUNGUNYA VIRUS ENVELOPE PROTEIN; GLYCOPROTEIN; PROTEIN INHIBITOR; UNCLASSIFIED DRUG; VIRUS ENVELOPE PROTEIN;

ALGORITHM; ARTICLE; BINDING SITE; CHIKUNGUNYA ALPHAVIRUS; COMPUTER MODEL; CRYSTAL STRUCTURE; MOLECULAR DOCKING; PRIORITY JOURNAL; PROTEIN BINDING; PROTEIN STRUCTURE; SCREENING;

ARBOVIRUS; CHIKUNGUNYA VIRUS;

ALPHAVIRUSES; CHIKUNGUNYA VIRUS; ENVELOPE PROTEINS; VIRTUAL SCREENING;

ANTIVIRAL AGENTS; BINDING SITES; CHIKUNGUNYA VIRUS; COMPUTER SIMULATION; DRUG DESIGN; HYDROGEN BONDING; MODELS, MOLECULAR; PROTEIN BINDING; PROTEIN CONFORMATION; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; VIRAL ENVELOPE PROTEINS;

EID: 84885132782     PISSN: 10933263     EISSN: 18734243     Source Type: Journal    
DOI: 10.1016/j.jmgm.2013.07.001     Document Type: Article

References (43)

1. Z. Her, Y.W. Kam, R.T. Lin, L.F. Ng, Chikungunya: a bending reality, Microbes and Infection 11 (2009) 1165-1176.
2. M.C. Robinson, An epidemic of virus disease in Southern Province, Tanganyika Territory, in 1952-53.I. Clinical features, Transactions of the Royal Society of Tropical Medicine and Hygiene 49 (1955) 28-32.
3. A.M. Powers, C.H. Logue, Changing patterns of chikungunya virus: re-emergence of a zoonotic arbovirus, Journal of General Virology 88 (2007) 2363-2377. (Pubitemid 47323881)
4. O. Schwartz, M.L. Albert, Biology and pathogenesis of chikungunya virus, Nature Reviews Microbiology 8 (2010) 491-500.
5. S.A. Ziegler, L. Lu, A.P. da Rosa, S.Y. Xiao, R.B. Tesh, An animal model for studying the pathogenesis of chikungunya virus infection, American Journal ofTropical Medicine and Hygiene 79 (2008) 133-139. (Pubitemid 351957217)
6. B. Queyriaux, F. Simon, M. Grandadam, R. Michel, H. Tolou, J.P. Boutin, Clinical burdenof chikungunya virus infection, Lancet Infectious Diseases 8 (2008) 2-3. (Pubitemid 351626997)
7. S.R. Santhosh, P.K. Dash, M.M. Parida, M. Khan, M. Tiwari, P.V. Lakshmana Rao, Comparative full genome analysis revealed E1: A226V shift in 2007 Indian Chikungunya virus isolates, Virus Research 135 (2008)36-41.
8. N.H. Chandak, R.S. Kashyap, D. Kabra, P. Karandikar, S.S. Saha, S.H. Morey, et al., Neurological complications of chikungunya virus infection, Neurology India 57 (2009)177-180.
9. S.K. Singh, S.K. Unni, Chikungunya virus: host pathogen interaction, Reviews in Medical Virology 21 (2011)78-88.
10. M. Sourisseau, C. Schilte, N. Casartelli, C. Trouillet, F. Guivel-Benhassine, D. Rud-nicka, et al., Characterization of reemerging chikungunya virus, PLoS Pathogens 3 (2007) e89.
11. P. Wintachai, N. Wikan, A. Kuadkitkan, T. Jaimipuk, S. Ubol, R. Pulmanausa-hakul, et al., Identification of prohibitin as a chikungunya virus receptor protein, Journal of Medical Virology 84 (2012) 1757-1770.
12. M. Kielian, FA Rey, Virus membrane-fusion proteins: more than one way to make a hairpin, Nature Reviews Microbiology 4 (2006) 67-76. (Pubitemid 43135288)
13. M. Marsh, A. Helenius, Virus entry: open sesame, Cell 124 (2006) 729-740. (Pubitemid 43261448)
14. B.L. Tang, The cell biology of Chikungunya virus infection, Cellular Microbiology 14 (2012)1354-1363.
15. A. Salminen, J.M. Wahlberg, M. Lobigs, P. Liljestrom, H. Garoff, Membrane fusion process of Semliki Forest virus. II: cleavage-dependent reorganization of the spike protein complex controls virus entry, Journal of Cell Biology 116 (1992) 349-357.
16. L. Li, J. Jose, Y. Xiang, R.J. Kuhn, M.G. Rossmann, Structural changes ofenvelope proteins during alphavirus fusion, Nature 468 (2010) 705-708.
17. J.E. Voss, M.C. Vaney, S. Duquerroy, C. Vonrhein, C. Girard-Blanc, E. Crublet, et al., Glycoprotein organization of Chikungunya virus particles revealed by X-ray crystallography, Nature 468 (2010) 709-712.
18. S. Ozden, M. Lucas-Hourani, P.E. Ceccaldi, A. Basak, M. Valentine, S. Benjannet, et al., Inhibition of Chikungunya virus infection in cultured human muscle cells by furin inhibitors: impairment of the maturation of the E2 surface glycoprotein, The Journal of Biological Chemistry 283 (2008) 21899-21908.
19. M. Lobigs, H.X. Zhao, H. Garoff, Function of Semliki Forest virus E3 peptide in virus assembly: replacement of E3 with an artificial signal peptide abolishes spike heterodimerization and surface expression of E1, Journal of Virology 64 (1990)4346-4355. (Pubitemid 20279845)
20. S.C. Kuo, Y.J. Chen, Y.M. Wang, P.Y. Tsui, M.D. Kuo, T.Y. Wu, et al., Cell-based analysis of Chikungunya virus E1 protein in membrane fusion, Journal of Biomedical Science 19 (2012) 44.
21. S. Briolant, D. Garin, N. Scaramozzino, A. Jouan, J.M. Crance, In vitro inhibition of Chikungunya and Semliki forest viruses replication by antiviral compounds: synergistic effect of interferon-alpha and ribavirin combination, Antiviral Research 61 (2004) 111-117. (Pubitemid 37506098)
22. X. de Lamballerie, L. Ninove, R.N. Charrel, Antiviral treatment of chikungunya virus infection, Infectious Disorders Drug Targets 9(2009) 101-104.
23. I. Delogu, B. Pastorino, C. Baronti, A. Nougairede, E. Bonnet, X. de Lamballerie, In vitro antiviral activity of arbidol against Chikungunya virus and characteristics of a selected resistant mutant, Antiviral Research 90 (2011) 99-107.
24. M. Khan, R. Dhanwani, I.K. Patro, P.V.L. Rao, M.M. Parida, Cellular IMPDH enzyme activity is a potential target for the inhibition of Chikungunya virus replication and virus induced apoptosis in cultured mammalian cells, Antiviral Research 89 (2011) 1-8.
25. L. Zhang, R.H. Luo, F. Wang, M.Y. Jiang, Z.J. Dong, L.M. Yang, et al., Highly func-tionalized daphnane diterpenoids from Trigonostemon thyrsoideum, Organic Letters 12 (2010) 152-155.
26. P. Kaur, M. Thiruchelvan, R.C. Lee, H. Chen, K.C. Chen, M.L. Ng, et al., Inhibition of chikungunya virus replication by harringtonine, a novel antiviral that suppresses viral protein expression, Antimicrobial Agents and Chemotherapy 57 (2013)155-167.
27. M. D'Hooghe, K. Mollet, R. De Vreese, T.H. Jonckers, G. Dams, N. De Kimpe, Design, synthesis, and antiviral evaluation of purine-beta-lactam and purine-aminopropanol hybrids, Journal of Medicinal Chemistry 55 (2012) 5637-5641.
28. Y.G. Li, U. Siripanyaphinyo, U. Tumkosit, N. Noranate, A.N. Atchareeya, Y. Pan, et al., Poly (I:C), an agonist of toll-like receptor-3, inhibits replication of the Chikungunya virus in BEAS-2B cells, Virology Journal 9 (2012) 114.
29. C. McInnes, Virtual screening strategies in drug discovery, Current Opinion in Chemical Biology 11 (2007) 494-502. (Pubitemid 47589008)
30. J. Kirchmair, S. Distinto, D. Schuster, G. Spitzer, T. Langer, G. Wolber, Enhancing drug discovery through in silico screening: strategies to increase true positives retrieval rates, Current Medicinal Chemistry 15 (2008) 2040-2053.
31. R. Yennamalli, N. Subbarao, T. Kampmann, R.P. McGeary, P.R. Young, B. Kobe, Identification of novel target sites and an inhibitor ofthe dengue virus E protein, Journal of Computer-Aided Molecular Design 23 (2009) 333-341.
32. Z.G. Zhou, M. Khaliq, J.E. Suk, C. Patkar, L. Li, R.J. Kuhn, et al., Antiviral compounds discovered by virtual screening of small-molecule libraries against dengue virus E protein, ACS Chemical Biology 3 (2008) 765-775.
33. Z. Li, M. Khaliq, Z.G. Zhou, C.B. Post, R.J. Kuhn, M. Cushman, Design, synthesis, and biological evaluation of antiviral agents targeting flavivirus envelope proteins, Journal of Medicinal Chemistry 51 (2008) 4660-4671.
34. CA. Lipinski, F. Lombardo, B.W. Dominy, P.J. Feeney, Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings, Advanced Drug Delivery Reviews 46 (2001) 3-26. (Pubitemid 33653411)
35. M. McGann, FRED pose prediction and virtual screening accuracy, Journal of Chemical Information and Modeling 51 (2011) 578-596.
36. G.B. McGaughey, R.P. Sheridan, CI. Bayly, J.C Culberson, C Kreatsoulas, S. Lindsley, et al., Comparison of topological, shape, and docking methods in virtual screening, Journal of Chemical Information and Modeling 47 (2007) 1504-1519. (Pubitemid 47210053)
37. M.R. McGann, H.R. Almond, A. Nicholls, J.A. Grant, F.K. Brown, Gaussian docking functions, Biopolymers 68 (2003) 76-90. (Pubitemid 36098309)
38. J. Bostrom, J.R. Greenwood, J. Gottfries, Assessing the performance of OMEGA with respect to retrieving bioactive conformations, Journal of MolecularGraph-ics and Modelling 21 (2003) 449-462. (Pubitemid 36120775)
39. P.C. Hawkins, A. Nicholls, Conformer generation with OMEGA: learning from the data set and the analysis of failures, Journal of Chemical Information and Modeling 52 (2012) 2919-2936.
40. G.M. Morris, R. Huey, W. Lindstrom, M.F. Sanner, R.K. Belew, D.S. Goodsell, et al., AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility, Journal of Computational Chemistry 30 (2009) 2785-2791.
41. D.B. Kitchen, H. Decornez, J.R. Furr, J. Bajorath, Docking and scoring in virtual screening for drug discovery: methods and applications, Nature Reviews Drug Discovery 3 (2004) 935-949. (Pubitemid 39529931)
42. H. Zaheer ul, S.A. Halim, R. Uddin, J.D. Madura, Benchmarking docking and scoring protocol forthe identification of potential acetylcholinesterase inhibitors, Journal of Molecular Graphics and Modelling 28 (2010) 870-882.
43. A.S. Mayhoub, M. Khaliq, R.J. Kuhn, M. Cushman, Design, synthesis, and biological evaluation of thiazoles targeting flavivirus envelope proteins, Journal of Medicinal Chemistry 54 (2011) 1704-1714.