Finding candidate drugs for hepatitis C based on chemical-chemical and chemical-protein interactions

PLoS ONE

Volumn 9, Issue 9, 2014, Pages

  Chen, Lei ^a   Lu, Jing ^b   Huang, Tao ^c   Yin, Jun ^a   Wei, Lai ^a   Cai, Yu Dong ^d  

^a SHANGHAI MARITIME UNIVERSITY   (China)

^b YANTAI UNIVERSITY   (China)

^c MOUNT SINAI SCHOOL OF MEDICINE   (United States)

^d SHANGHAI UNIVERSITY   (China)

Author keywords

[No Author keywords available]

Indexed keywords

ACICLOVIR; ATORVASTATIN; AZAURIDINE; BOCEPREVIR; CARFILZOMIB; CASTANOSPERMINE 6 BUTYRATE; DASATINIB; ETORICOXIB; FLUINDOSTATIN; GANCICLOVIR; GUANOSINE TRIPHOSPHATE; IMATINIB; MIGLUSTAT; PERIFOSINE; RASAGILINE; RIBAVIRIN; SORAFENIB; TELAPREVIR; TORCETRAPIB; VANDETANIB; ZALCITABINE; ZIDOVUDINE; ANTIVIRUS AGENT;

ALGORITHM; ANTIVIRAL ACTIVITY; ARTICLE; CHEMICAL CHEMICAL INTERACTION; CHEMICAL INTERACTION; CHEMICAL PROTEIN INTERACTION; DRUG CHOICE; DRUG EFFICACY; DRUG INDICATION; DRUG REPOSITIONING; EXPECTATION MAXIMIZATION ALGORITHM; HEPATITIS C; MATHEMATICAL COMPUTING; NONHUMAN; PREDICTION; PROBABILITY; PROTEIN INTERACTION; STATISTICAL ANALYSIS; BIOLOGY; DRUG DEVELOPMENT; DRUG EFFECTS; GENE EXPRESSION REGULATION; GENETICS; HEPACIVIRUS; HUMAN; METABOLISM; PROCEDURES;

HEPATITIS C VIRUS;

ALGORITHMS; ANTIVIRAL AGENTS; COMPUTATIONAL BIOLOGY; DRUG DISCOVERY; GENE EXPRESSION REGULATION, VIRAL; HEPACIVIRUS; HUMANS;

EID: 84907190397     PISSN: None     EISSN: 19326203     Source Type: Journal    
DOI: 10.1371/journal.pone.0107767     Document Type: Article

References (48)

1. Chander G, Sulkowski MS, Jenckes MW, Torbenson MS, Herlong HF, et al. (2002) Treatment of chronic hepatitis C: a systematic review. Hepatology 36: S135-144.
2. Approval of Incivek (telaprevir), a direct acting antiviral drug (DAA) to treat hepatitis C (HCV). Available: http://www.fda.gov/ForConsumers/ ByAudience/ForPatientAdvocates/ucm256328.htm. Accessed 2014 March 7.
3. Approval of Victrelis (boceprevir) a direct acting antiviral drug (DAA) to treat hepatitis C virus (HCV). Available: http://www.fda.gov/ForConsumers/ByAudience/ForPatientAdvocates/ucm255413.htm. Accessed 2014 March 7.
4. Zhu Y, Chen S (2013) Antiviral treatment of hepatitis C virus infection and factors affecting efficacy. World J Gastroenterol 19: 8963-8973.
5. Zheng M, Liu Z, Xue C, Zhu W, Chen K, et al. (2006) Mutagenic probability estimation of chemical compounds by a novel molecular electrophilicity vector and support vector machine. Bioinformatics 22: 2099-2106.
6. Wang Y, Lu J, Wang F, Shen Q, Zheng M, et al. (2012) Estimation of carcinogenicity using molecular fragments tree. J Chem Inf Model 52: 1994-2003.
7. Lu J, Zheng M, Wang Y, Shen Q, Luo X, et al. (2011) Fragment-based prediction of skin sensitization using recursive partitioning. Journal of computer-aided molecular design 25: 885-893.
8. Weidlich IE, Filippov IV, Brown J, Kaushik-Basu N, Krishnan R, et al. (2013) Inhibitors for the hepatitis C virus RNA polymerase explored by SAR with advanced machine learning methods. Bioorg Med Chem 21: 3127-3137.
9. Wang M, Zhong M, Yan A, Li L, Yu C (2014) Quantitative structure and bioactivity relationship study on HCV NS5B polymerase inhibitors. SAR QSAR Environ Res 25: 1-15.
10. Speck-Planche A, Cordeiro MDS (2012) Computer-Aided Drug Design Methodologies Toward the Design of Anti-Hepatitis C Agents. Current Topics in Medicinal Chemistry 12: 802-813
11. Kuhn M, von Mering C, Campillos M, Jensen LJ, Bork P (2008) STITCH: interaction networks of chemicals and proteins. Nucleic Acids Res 36: D684-688.
12. Lu J, Huang G, Li HP, Feng KY, Chen L, et al. (2014) Prediction of cancer drugs by chemical-chemical interactions. PLoS One 9: e87791.
13. Chen L, Lu J, Zhang N, Huang T, Cai YD (2014) A hybrid method for prediction and repositioning of drug Anatomical Therapeutic Chemical classes. Molecular BioSystems 10: 868-877.
14. Chen L, Zeng WM, Cai YD, Feng KY, Chou KC (2012) Predicting Anatomical Therapeutic Chemical (ATC) Classification of Drugs by Integrating Chemical-Chemical Interactions and Similarities. PLoS ONE 7: e35254.
15. Hu LL, Chen C, Huang T, Cai YD, Chou KC (2011) Predicting Biological Functions of Compounds Based on Chemical-Chemical Interactions. PLoS ONE 6: e29491.
16. Chen L, Lu J, Luo X, Feng KY (2014) Prediction of drug target groups based on chemical-chemical similarities and chemical-chemical/protein connections. Biochimica et Biophysica Acta (BBA)-Proteins and Proteomics 1844: 207-213.
17. Wishart DS, Knox C, Guo AC, Cheng D, Shrivastava S, et al. (2008) DrugBank: a knowledgebase for drugs, drug actions and drug targets. Nucleic acids research 36: D901-D906.
18. Wishart DS, Knox C, Guo AC, Shrivastava S, Hassanali M, et al. (2006) DrugBank: a comprehensive resource for in silico drug discovery and exploration. Nucleic acids research 34: D668-D672.
19. De Chassey B, Navratil V, Tafforeau L, Hiet M, Aublin-Gex A, et al. (2008) Hepatitis C virus infection protein network. Molecular systems biology 4: 230.
20. Huang T, Wang J, Cai YD, Yu H, Chou KC (2012) Hepatitis C virus network based classification of hepatocellular cirrhosis and carcinoma. PLoS ONE 7: e34460.
21. Jiang M, Chen Y, Zhang Y, Chen L, Zhang N, et al. (2013) Identification of hepatocellular carcinoma related genes with k-th shortest paths in a protein-protein interaction network. Mol BioSyst 9: 2720-2728.
22. Li BQ, Huang T, Liu L, Cai YD, Chou KC (2012) Identification of Colorectal Cancer Related Genes with mRMR and Shortest Path in Protein-Protein Interaction Network. PLoS One 7: e33393.
23. Dempster AP, Laird NM, Rubin DB (1977) Maximum likelihood from incomplete data via the EM algorithm. Journal of the Royal Statistical Society, Series B 39: 1-38.
24. Witten IH, Frank E (2005) Data Mining: Practical machine learning tools and techniques: Morgan Kaufmann Pub.
25. Johnson MA, Maggiora GM, editors (1990) Concepts and Applications of Molecular Similarity. New York: John Wiley & Sons.
26. Aciclovir website. Available: http://www.drugbank.ca/drugs/DB00787. Accessed 2014 June 11.
27. Ganciclovir website. Available: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=3454. Accessed 2014 June 11.
28. 1986-1990 Hepatitis C Claims Centre Hcv Medication List. Available: http://www.hepc8690.ca/content/claimants/additional/HCV%20Medication%20List-e.shtml. Accessed 2014 June 11.
29. Sorafenib website. Available: http://www.drugbank.ca/drugs/DB00398. Accessed 2014 June 12.
30. Himmelsbach K, Sauter D, Baumert TF, Ludwig L, Blum HE, et al. (2009) New aspects of an anti-tumour drug: sorafenib efficiently inhibits HCV replication. Gut 58: 1644-1653.
31. Himmelsbach K, Hildt E (2013) The kinase inhibitor Sorafenib impairs the antiviral effect of interferon alpha on hepatitis C virus replication. Eur J Cell Biol 92: 12-20.
32. Fluvastatin website. Available: http://www.drugbank.ca/drugs/DB01095. Accessed 2014 June 16.
33. Bader T, Fazili J, Madhoun M, Aston C, Hughes D, et al. (2008) Fluvastatin inhibits hepatitis C replication in humans. Am J Gastroenterol 103: 1383-1389.
34. Fluvastatin enhances chronic heptatitis C treatment response in combination with pegylated Interferon-Alpha and Ribavirin. Available: http://www.easl.eu/-newsroom/press-release/fluvastatin-enhances-chronic-heptatitis-c-treatment-response-in-combination-with-pegylated-interferon-alpha-and-ribavirin. Accessed 2014 June 16.
35. de Bruijne J, Weegink CJ, Jansen PL, Reesink HW (2009) New developments in the antiviral treatment of hepatitis C. Vox Sang 97: 1-12.
36. Yoshida E, Kunimoto D, Lee SS, Sherman M, Heathcote J, et al. (2006) Results of a Phase II dose ranging study of orally administered celgosivir as monotherapy in chronic hepatitis C genotype-1 patients. Gastroenterology 130: A784 (abstract S1059).
37. Kaita K, Yoshida E, Kunimoto D, Anderson F, Morris S, et al. (2007) Phil PROOF OF CONCEPT STUDY OF CELGOSIVIR IN COMBINATION WITH PEGINTERFERON o-2b AND RIBAVIRIN IN CHRONIC HEPATITIS C GENOTYPE-1 NON-RESPONDER PATIENTS. Journal of Hepatology 46: S56-S57.
38. Miglustat website. Available: http://www.drugbank.ca/drugs/DB00419. Accessed 2014 June 17.
39. Hepatitis C: Review of Current Treatments and Market Opportunities. Available: http://drugdiscoveryopinion.com/downloads/HepatitisC.pdf. Accessed 2014 June 12.
40. Advances in treatment HCV. Available: http://www.fitwise.co.uk/files/8613/8727/5651/Thur-Session7-JDillon.pdf. Accessed 2014 June 12.
41. Dasatinib website. Available: http://www.drugbank.ca/drugs/DB01254. Accessed 2014 June 19.
42. McCartney EM, Eyre NS, Beard MR (2011) Border patrol intensifies for hepatitis C virus entry. Hepatology 54: 1472-1475.
43. Lupberger J, Zeisel MB, Xiao F, Thumann C, Fofana I, et al. (2011) EGFR and EphA2 are host factors for hepatitis C virus entry and possible targets for antiviral therapy. Nat Med 17: 589-595.
44. Ikeda M, Abe K, Yamada M, Dansako H, Naka K, et al. (2006) Different anti-HCV profiles of statins and their potential for combination therapy with interferon. Hepatology 44: 117-125.
45. Zidovudine website. Available: http://www.drugbank.ca/drugs/DB00495. Accessed 2014 June 10.
46. Vento S, Garofano T, Di Perri G, Cruciani M, Concia E, et al. (1991) Zidovudine therapy associated with remission of chronic active hepatitis C in HIV-1 carriers. AIDS 5: 776.
47. Azauridine website. Available: http://pubchem.ncbi.nlm.nih.gov/summary/summary.cgi?cid=5901&loc=ec-rcs. Accessed 2014 June 11.
48. Ueda Y, Mori K, Ariumi Y, Ikeda M, Kato N (2011) Plural assay systems derived from different cell lines and hepatitis C virus strains are required for the objective evaluation of anti-hepatitis C virus reagents. Biochem Biophys Res Commun 409: 663-668.