New horizons for antiviral drug discovery from virus-host protein interaction networks

Current Opinion in Virology

Volumn 2, Issue 5, 2012, Pages 606-613

  De Chassey, Benoît ^a,b   Meyniel Schicklin, Laurène ^a,b   Aublin Gex, Anne ^a,b   André, Patrice ^a,b,c   Lotteau, Vincent ^a,b,c  

^a UNIVERSITÉ DE LYON   (France)

^b INSERM   (France)

^c CROIX ROUSSE HOSPITAL   (France)

Author keywords

[No Author keywords available]

Indexed keywords

ANTIVIRUS AGENT; CELL PROTEIN; DAS 181; GELDANAMYCIN; HOST FACTOR; MARAVIROC; TG 003; UNCLASSIFIED DRUG;

ARTICLE; DENGUE VIRUS; DRUG DEVELOPMENT; DRUG RESEARCH; DRUG TARGETING; HEPATITIS C VIRUS; HUMAN; HUMAN IMMUNODEFICIENCY VIRUS; INFLUENZA VIRUS; INNATE IMMUNITY; NONHUMAN; PRIORITY JOURNAL; VIRUS CELL INTERACTION; VIRUS INFECTION;

EID: 84867396470     PISSN: 18796257     EISSN: 18796265     Source Type: Journal    
DOI: 10.1016/j.coviro.2012.09.001     Document Type: Review

References (56)

1. A.C. Hurt, T. Chotpitayasunondh, N.J. Cox, R. Daniels, A.M. Fry, L.V. Gubareva, F.G. Hayden, D.S. Hui, O. Hungnes, and A. Lackenby Antiviral resistance during the 2009 influenza A H1N1 pandemic: public health, laboratory, and clinical perspectives Lancet Infectious Diseases 12 2012 240 248
2. A. Chatr-aryamontri, A. Ceol, D. Peluso, A. Nardozza, S. Panni, F. Sacco, M. Tinti, A. Smolyar, L. Castagnoli, and M. Vidal VirusMINT: a viral protein interaction database Nucleic Acids Research 37 2009 D669 D673
3. V. Navratil, B. de Chassey, L. Meyniel, S. Delmotte, C. Gautier, P. Andre, V. Lotteau, and C. Rabourdin-Combe VirHostNet: a knowledge base for the management and the analysis of proteome-wide virus-host interaction networks Nucleic Acids Research 37 2009 D661 D668
4. International Human Genome Sequencing Consortium Finishing the euchromatic sequence of the human genome Nature 431 2004 931 945
5. J. Pellet, L. Tafforeau, M. Lucas-Hourani, V. Navratil, L. Meyniel, G. Achaz, A. Guironnet-Paquet, A. Aublin-Gex, G. Caignard, and P. Cassonnet ViralORFeome: an integrated database to generate a versatile collection of viral ORFs Nucleic Acids Research 38 2010 D371 D378
6. P. Lamesch, N. Li, S. Milstein, C. Fan, T. Hao, G. Szabo, Z. Hu, K. Venkatesan, G. Bethel, and P. Martin hORFeome v3.1: a resource of human open reading frames representing over 10,000 human genes Genomics 89 2007 307 315
7. S.M. Bailer, and J. Haas Connecting viral with cellular interactomes Current Opinion in Microbiology 12 2009 453 459
8. H. Yu, P. Braun, M.A. Yildirim, I. Lemmens, K. Venkatesan, J. Sahalie, T. Horizane-Kishikawa, F. Gebreab, N. Li, and N. Simonis High-quality binary protein interaction map of the yeast interactome network Science 322 2008 104 110
9. M.A. Calderwood, K. Venkatesan, L. Xing, M.R. Chase, A. Vazquez, A.M. Holthaus, A.E. Ewence, N. Li, T. Hirozane-Kishikawa, and D.E. Hill Epstein-Barr virus and virus human protein interaction maps Proceedings of the National Academy of Sciences of the United States of America 104 2007 7606 7611
10. B. de Chassey, V. Navratil, L. Tafforeau, M.S. Hiet, A. Aublin-Gex, S. Agaugue, G. Meiffren, F. Pradezynski, B.F. Faria, and T. Chantier Hepatitis C virus infection protein network Molecular Systems Biology 4 2008 230
11. S. Khadka, A.D. Vangeloff, C. Zhang, P. Siddavatam, N.S. Heaton, L. Wang, R. Sengupta, S. Sahasrabudhe, G. Randall, and M. Gribskov A physical interaction network of dengue virus and human proteins Molecular and Cellular Proteomics 10 2011 M111 012187
12. S.D. Shapira, I. Gat-Viks, B.O. Shum, A. Dricot, M.M. de Grace, L. Wu, P.B. Gupta, T. Hao, S.J. Silver, and D.E. Root A physical and regulatory map of host-influenza interactions reveals pathways in H1N1 infection Cell 139 2009 1255 1267
13. L. Zhang, N.Y. Villa, M.M. Rahman, S. Smallwood, D. Shattuck, C. Neff, M. Dufford, J.S. Lanchbury, J. Labaer, and G. McFadden Analysis of vaccinia virus-host protein-protein interactions: validations of yeast two-hybrid screenings Journal of Proteome Research 8 2009 4311 4318
14. S. Jager, P. Cimermancic, N. Gulbahce, J.R. Johnson, K.E. McGovern, S.C. Clarke, M. Shales, G. Mercenne, L. Pache, and K. Li Global landscape of HIV-human protein complexes Nature 481 2012 365 370
15. P. Braun, M. Tasan, M. Dreze, M. Barrios-Rodiles, I. Lemmens, H. Yu, J.M. Sahalie, R.R. Murray, L. Roncari, and A.S. de Smet An experimentally derived confidence score for binary protein-protein interactions Nature Methods 6 2009 91 97
16. L. Meyniel-Schicklin, B. de Chassey, P. Andre, and V. Lotteau Viruses and interactomes in translation Molecular and Cellular Proteomics 11 2012 M111 014738
17. L. Hao, A. Sakurai, T. Watanabe, E. Sorensen, C.A. Nidom, M.A. Newton, P. Ahlquist, and Y. Kawaoka Drosophila RNAi screen identifies host genes important for influenza virus replication Nature 454 2008 890 893
18. R. Konig, S. Stertz, Y. Zhou, A. Inoue, H.H. Hoffmann, S. Bhattacharyya, J.G. Alamares, D.M. Tscherne, M.B. Ortigoza, and Y. Liang Human host factors required for influenza virus replication Nature 463 2010 813 817
19. A. Karlas, N. Machuy, Y. Shin, K.P. Pleissner, A. Artarini, D. Heuer, D. Becker, H. Khalil, L.A. Ogilvie, and S. Hess Genome-wide RNAi screen identifies human host factors crucial for influenza virus replication Nature 463 2010 818 822
20. A.L. Brass, D.M. Dykxhoorn, Y. Benita, N. Yan, A. Engelman, R.J. Xavier, J. Lieberman, and S.J. Elledge Identification of host proteins required for HIV infection through a functional genomic screen Science 319 2008 921 926
21. R. Konig, Y. Zhou, D. Elleder, T.L. Diamond, G.M. Bonamy, J.T. Irelan, C.Y. Chiang, B.P. Tu, P.D. De Jesus, and C.E. Lilley Global analysis of host-pathogen interactions that regulate early-stage HIV-1 replication Cell 135 2008 49 60
22. H. Zhou, M. Xu, Q. Huang, A.T. Gates, X.D. Zhang, J.C. Castle, E. Stec, M. Ferrer, B. Strulovici, and D.J. Hazuda Genome-scale RNAi screen for host factors required for HIV replication Cell Host & Microbe 4 2008 495 504
23. Q. Li, A.L. Brass, A. Ng, Z. Hu, R.J. Xavier, T.J. Liang, and S.J. Elledge A genome-wide genetic screen for host factors required for hepatitis C virus propagation Proceedings of the National Academy of Sciences of the United States of America 106 2009 16410 16415
24. A.W. Tai, Y. Benita, L.F. Peng, S.S. Kim, N. Sakamoto, R.J. Xavier, and R.T. Chung A functional genomic screen identifies cellular cofactors of hepatitis C virus replication Cell Host & Microbe 5 2009 298 307
25. O.M. Sessions, N.J. Barrows, J.A. Souza-Neto, T.J. Robinson, C.L. Hershey, M.A. Rodgers, J.L. Ramirez, G. Dimopoulos, P.L. Yang, and J.L. Pearson Discovery of insect and human dengue virus host factors Nature 458 2009 1047 1050
26. M.N. Krishnan, A. Ng, B. Sukumaran, F.D. Gilfoy, P.D. Uchil, H. Sultana, A.L. Brass, R. Adametz, M. Tsui, and F. Qian RNA interference screen for human genes associated with West Nile virus infection Nature 455 2008 242 245
27. B. de Chassey, L. Meyniel-Schicklin, A. Aublin-Gex, P. Andre, and V. Lotteau Genetic screens for the control of influenza virus replication: from meta-analysis to drug discovery Molecular BioSystems 8 2012 1297 1303
28. F.D. Bushman, N. Malani, J. Fernandes, I. D'Orso, G. Cagney, T.L. Diamond, H. Zhou, D.J. Hazuda, A.S. Espeseth, and R. König Host cell factors in HIV replication: meta-analysis of genome-wide studies PLoS Pathogens 5 2009 e1000437
29. S. Stertz, and M.L. Shaw Uncovering the global host cell requirements for influenza virus replication via RNAi screening Microbes and Infection 13 2011 516 525
30. B. Turner, S. Razick, A.L. Turinsky, J. Vlasblom, E.K. Crowdy, E. Cho, K. Morrison, I.M. Donaldson, and S.J. Wodak iRefWeb: interactive analysis of consolidated protein interaction data and their supporting evidence Database (Oxford) 2010 2010 baq023
31. A.L. Barabasi, and Z.N. Oltvai Network biology: understanding the cell's functional organization Nature Reviews. Genetics 5 2004 101 113
32. R. Albert, H. Jeong, and A.L. Barabasi Error and attack tolerance of complex networks Nature 406 2000 378 382
33. R. Cohen, and S. Havlin Scale-free networks are ultrasmall Physical Review Letters 90 2003 058701
34. M.D. Dyer, T.M. Murali, and B.W. Sobral The landscape of human proteins interacting with viruses and other pathogens PLoS Pathogens 4 2008 e32
35. V. Navratil, B. de Chassey, C.R. Combe, and V. Lotteau When the human viral infectome and diseasome networks collide: towards a systems biology platform for the aetiology of human diseases BMC Systems Biology 5 2011 13
36. D.J. Lynn, G.L. Winsor, C. Chan, N. Richard, M.R. Laird, A. Barsky, J.L. Gardy, F.M. Roche, T.H. Chan, and N. Shah InnateDB: facilitating systems-level analyses of the mammalian innate immune response Molecular Systems Biology 4 2008 218
37. K. Oda, and H. Kitano A comprehensive map of the toll-like receptor signaling network Molecular Systems Biology 2 2006 0015
38. J. Stack, I.R. Haga, M. Schroder, N.W. Bartlett, G. Maloney, P.C. Reading, K.A. Fitzgerald, G.L. Smith, and A.G. Bowie Vaccinia virus protein A46R targets multiple Toll-like-interleukin-1 receptor adaptors and contributes to virulence Journal of Experimental Medicine 201 2005 1007 1018
39. T. Abe, Y. Kaname, I. Hamamoto, Y. Tsuda, X. Wen, S. Taguwa, K. Moriishi, O. Takeuchi, T. Kawai, and T. Kanto Hepatitis C virus nonstructural protein 5A modulates the toll-like receptor-MyD88-dependent signaling pathway in macrophage cell lines Journal of Virology 81 2007 8953 8966
40. V. Navratil, B. de Chassey, L. Meyniel, F. Pradezynski, P. Andre, C. Rabourdin-Combe, and V. Lotteau System-level comparison of protein-protein interactions between viruses and the human type I interferon system network Journal of Proteome Research 9 2010 3527 3536
41. B. Levine, N. Mizushima, and H.W. Virgin Autophagy in immunity and inflammation Nature 469 2011 323 335
42. I.P. Gregoire, C. Richetta, L. Meyniel-Schicklin, S. Borel, F. Pradezynski, O. Diaz, A. Deloire, O. Azocar, J. Baguet, and M. Le Breton IRGM is a common target of RNA viruses that subvert the autophagy network PLoS Pathogens 7 2011 e1002422
43. C. Behrends, M.E. Sowa, S.P. Gygi, and J.W. Harper Network organization of the human autophagy system Nature 466 2010 68 76
44. P. Dorr, M. Westby, S. Dobbs, P. Griffin, B. Irvine, M. Macartney, J. Mori, G. Rickett, C. Smith-Burchnell, and C. Napier Maraviroc (UK-427,857), a potent, orally bioavailable, and selective small-molecule inhibitor of chemokine receptor CCR5 with broad-spectrum anti-human immunodeficiency virus type 1 activity Antimicrobial Agents and Chemotherapy 49 2005 4721 4732
45. J.A. Belser, X. Lu, K.J. Szretter, X. Jin, L.M. Aschenbrenner, A. Lee, S. Hawley, H. Kim do, M.P. Malakhov, and M. Yu DAS181, a novel sialidase fusion protein, protects mice from lethal avian influenza H5N1 virus infection Journal of Infectious Diseases 196 2007 1493 1499
46. L. Diaz, H. Mao, Y. Zhou, M. Kohli, J. Cassella, D. Santos, Z. Fesseha, K. Weng, H. Chen, and D. Bamba TSG101 exposure on the surface of HIV-1 infected cells: implications for monoclonal antibody therapy for HIV/AIDS American Journal of Translational Research 2 2010 368 380
47. T.T. Ashburn, and K.B. Thor Drug repositioning: identifying and developing new uses for existing drugs Nature Reviews. Drug Discovery 3 2004 673 683
48. S.S. Kim, L.F. Peng, W. Lin, W.H. Choe, N. Sakamoto, N. Kato, M. Ikeda, S.L. Schreiber, and R.T. Chung A cell-based, high-throughput screen for small molecule regulators of hepatitis C virus replication Gastroenterology 132 2007 311 320
49. H.H. Hoffmann, P. Palese, and M.L. Shaw Modulation of influenza virus replication by alteration of sodium ion transport and protein kinase C activity Antiviral Research 80 2008 124 134
50. D.A. Patel, A.C. Patel, W.C. Nolan, Y. Zhang, and M.J. Holtzman High throughput screening for small molecule enhancers of the interferon signaling pathway to drive next-generation antiviral drug discovery PLoS ONE 7 2012 e36594
51. J.P. Overington, B. Al-Lazikani, and A.L. Hopkins How many drug targets are there? Nature Reviews. Drug Discovery 5 2006 993 996
52. P. Cassonnet, C. Rolloy, G. Neveu, P.O. Vidalain, T. Chantier, J. Pellet, L. Jones, M. Muller, C. Demeret, and G. Gaud Benchmarking a luciferase complementation assay for detecting protein complexes Nature Methods 8 2011 990 992
53. M. Barrios-Rodiles, K.R. Brown, B. Ozdamar, R. Bose, Z. Liu, R.S. Donovan, F. Shinjo, Y. Liu, J. Dembowy, and I.W. Taylor High-throughput mapping of a dynamic signaling network in mammalian cells Science 307 2005 1621 1625
54. S. Lievens, N. Vanderroost, D. Defever, J. Van der Heyden, and J. Tavernier ArrayMAPPIT: a screening platform for human protein interactome analysis Methods in Molecular Biology 812 2012 283 294
55. A. Mullard Protein-protein interaction inhibitors get into the groove Nature Reviews. Drug Discovery 11 2012 173 175
56. N.E. Davey, R.J. Edwards, and D.C. Shields Computational identification and analysis of protein short linear motifs Frontiers in Bioscience 15 2010 801 825