Classification of HCV NS5B polymerase inhibitors using support vector machine

International Journal of Molecular Sciences

Volumn 13, Issue 4, 2012, Pages 4033-4047

  Wang, Maolin ^a   Wang, Kai ^a   Yan, Aixia ^a   Yu, Changyuan ^a  

^a BEIJING UNIVERSITY OF CHEMICAL TECHNOLOGY   (China)

Author keywords

Classification models; Hepatitis C virus (HCV); NS5B polymerase inhibitor; Support vector machine (SVM)

Indexed keywords

ACRYLIC ACID DERIVATIVE; ANTIVIRUS AGENT; BENZOTHIADIAZINE DERIVATIVE; BENZYLIDENE DERIVATIVE; NONSTRUCTURAL PROTEIN 5B; NONSTRUCTURAL PROTEIN 5B POLYMERASE INHIBITOR; PYRROLIDINE DERIVATIVE; SULFONAMIDE; UNCLASSIFIED DRUG; NS-5 PROTEIN, HEPATITIS C VIRUS; VIRUS PROTEIN;

ACCURACY; ARTICLE; COMPUTER PROGRAM; CONTROLLED STUDY; CORRELATION COEFFICIENT; DRUG BINDING SITE; DRUG CLASSIFICATION; DRUG PROTEIN BINDING; HEPATITIS C VIRUS; HYDROGEN BOND; IC 50; MOLECULAR SIZE; PREDICTION; SOLUBILITY; SUPPORT VECTOR MACHINE; ANTAGONISTS AND INHIBITORS; BINDING SITE; DRUG DEVELOPMENT; DRUG EFFECTS; ENZYMOLOGY; HEPACIVIRUS; HEPATITIS C, CHRONIC; PROCEDURES;

BINDING SITES; DRUG DISCOVERY; HEPACIVIRUS; HEPATITIS C, CHRONIC; SUPPORT VECTOR MACHINES; VIRAL NONSTRUCTURAL PROTEINS;

EID: 84860135197     PISSN: None     EISSN: 14220067     Source Type: Journal    
DOI: 10.3390/ijms13044033     Document Type: Article

References (38)

1. Koch, U.; Attenni, B.; Malancona, S.; Colarusso, S.; Conte, I.; di Filippo, M.; Harper, S.; Pacini, B.; Giomini, C.; Thomas, S.; et al. 2-(2-Thienyl)-5,6-dihydroxy-4-carboxypyrimidines as inhibitors of the hepatitis C virus NS5B polymerase: Discovery, SAR, modeling, and mutagenesis. J. Med. Chem. 2006, 49, 1693-1705.
2. Tedesco, R.; Shaw, A.N.; Bambal, R.; Chai, D.; Concha, N.O.; Darcy, M.G.; Dhanak, D.; Fitch, D.M.; Gates, A.; Gerhardt, W.G.; et al. 3-(1,1-dioxo-2H-(1,2,4)-benzothiadiazin-3-yl)-4-hydroxy-2(1H)-quinolinones, potent inhibitors of hepatitis C virus RNA-dependent RNA polymerase. J. Med. Chem. 2006, 49, 971-983.
3. Ontoria, J.M.; Rydberg, E.H.; di Marco, S.; Tomei, L.; Attenni, B.; Malancona, S.; Hernando, J.I.M.; Gennari, N.; Koch, U.; Narjes, F.; et al. Identification and biological evaluation of a series of 1H-benzo[de]isoquinoline-1,3(2H)-diones as hepatitis C virus NS5B polymerase inhibitors. J. Med. Chem. 2009, 52, 5217-5227.
4. Chen, K.X.; Lesburg, C.A.; Vibulbhan, B.; Yang, W. A novel class of highly potent irreversible hepatitis C virus NS5B polymerase inhibitors. J. Med. Chem. 2012, 55, 2089-2101.
5. Krueger, A.C.; Madigan, D.L.; Jiang, W.W.; Kati, W.M.; Liu, D.; Liu, Y.; Maring, C.J.; Masse, S.; McDaniel, K.F.; Middleton, T.; et al. Inhibitors of HCV NS5B polymerase: Synthesis and structure-activity relationships of N-alkyl-4-hydroxyquinolon-3-yl-benzothiadiazine sulfamides. Bioorg. Med. Chem. Lett. 2006, 16, 3367-3370.
6. Ishida, T.; Suzuki, T.; Hirashima, S.; Mizutani, K.; Yoshida, A.; Ando, I.; Ikeda, S.; Adachi, T.; Hashimoto, H. Benzimidazole inhibitors of hepatitis C virus NS5B polymerase: Identification of 2-[(4-diarylmethoxy)phenyl]-benzimidazole. Bioorg. Med. Chem. Lett. 2006, 16, 1859-1863.
7. Das, D.; Hong, J.; Chen, S.H.; Wang, G.; Beigelman, L.; Seiwert, S.D.; Buckman, B.O. Recent advances in drug discovery of benzothiadiazine and related analogs as HCV NS5B polymerase inhibitors. Bioorg. Med. Chem. 2011, 19, 4690-4703.
8. Pfefferkorn, J.A.; Greene, M.L.; Nugent, R.A.; Gross, R.J.; Mitchell, M.A.; Finzel, B.C.; Harris, M.S.; Wells, P.A.; Shelly, J.A.; Anstadt, R.A.; et al. Inhibitors of HCV NS5B polymerase. Part 1: Evaluation of the southern region of (2Z)-2-(benzoylamino)-3-(5-phenyl-2-furyl)acrylic acid. Bioorg. Med. Chem. Lett. 2005, 15, 2481-2486.
9. Donner, P.L.; Xie, Q.; Pratt, J.K.; Maring, C.J.; Kati, W.; Jiang, W.; Liu, Y.; Koev, G.; Masse, S.; Montgomery, D.; et al. Des-A-ring benzothiadiazines: Inhibitors of HCV genotype 1 NS5B RNA-dependent RNA polymerase. Bioorg. Med. Chem. Lett. 2008, 18, 2735-2738.
10. Powdrill, M.H.; Bernatchez, J.A.; Gotte, M. Inhibitors of the hepatitis C virus RNA-dependent RNA polymerase NS5B. Viruses 2010, 2, 2169-2195.
11. Wang, Z.; Chen, Y.; Liang, H.; Bender, A.; Glen, R.C.; Yan, A. P-glycoprotein substrate models using support vector machines based on a comprehensive data set. J. Chem. Inf. Model. 2011, 51, 1447-1456.
12. Subramaniam, S.; Mehrotra, M.; Gupta, D. Support vector machine based classification model for screening Plasmodium falciparum proliferation Inhibitors and non-inhibitors. Biomed. Eng. Comput. Biol. 2011, 3, 13-24.
13. Liew, C.Y.; Ma, X.H.; Liu, X.; Yap, C.W. SVM model for virtual screening of Lck inhibitors. J. Chem. Inf. Model. 2009, 49, 877-885.
14. Armutlu, P.; Ozdemir, M.E.; Uney-Yuksektepe, F.; Kavakli, I.H.; Turkay, M. Classification of drug molecules considering their IC50 values using mixed-integer linear programming based hyper-boxes method. BMC Bioinforma. 2008, 9, doi:10.1186/1471-2105-9-411.
15. Hao, M.; Li, Y.; Wang, Y.; Zhang, S. A classification study of respiratory syncytial virus (RSV) inhibitors by variable selection with random forest. Int. J. Mol. Sci. 2011, 12, 1259-1280.
16. Lv, W.; Xue, Y. Prediction of hepatitis c virus non-structural proteins 5B polymerase inhibitors using machine learning methods. Acta Phys. Chim. Sin. 2011, 27, 1407-1416.
17. ADRIANA.Code, Molecular Networks GmbH, Erlangen, Germany. Available online: http://www.molecular-networks.com (accessed on 22 March 2012).
18. Gasteiger, J.; Jochum, C. An algorithm for the perception of synthetically important rings. J. Chem. Inf. Comput. Sci. 1979, 19, 43-48.
19. Todeschini, R.; Consonni, V. Handbook of Molecular Descriptors; Wiley-VCH: Weinheim, Germany, 2000; Volume 11.
20. Pfefferkorn, J.A.; Nugent, R.; Gross, R.J.; Greene, M.; Mitchell, M.A.; Reding, M.T.; Funk, L.A.; Anderson, R.; Wells, P.A.; Shelly, J.A.; et al. Inhibitors of HCV NS5B polymerase. Part 2: Evaluation of the northern region of (2Z)-2-benzoylamino-3-(4-phenoxy-phenyl)-acrylic acid. Bioorg. Med. Chem. Lett. 2005, 15, 2812-2818.
21. Zhou, Y.; Webber, S.E.; Murphy, D.E.; Li, L.S.; Dragovich, P.S.; Tran, C.V.; Sun, Z.; Ruebsam, F.; Shah, A.M.; Tsan, M.; et al. Novel HCV NS5B polymerase inhibitors derived from 4-(1',1'-dioxo-1',4'-dihydro-1'lambda6-benzo[1',2',4']thiadiazin-3'-yl)-5-hydroxy-2H-pyridazin-3-ones. Part 1: Exploration of 7'-substitution of benzothiadiazine. Bioorg. Med. Chem. Lett. 2008, 18, 1413-1418.
22. Burton, G.; Ku, T.W.; Carr, T.J.; Kiesow, T.; Sarisky, R.T.; Lin-Goerke, J.; Baker, A.; Earnshaw, D.L.; Hofmann, G.A.; Keenan, R.M.; et al. Identification of small molecule inhibitors of the hepatitis C virus RNA-dependent RNA polymerase from a pyrrolidine combinatorial mixture. Bioorg. Med. Chem. Lett. 2005, 15, 1553-1556.
23. De Vicente, J.; Hendricks, R.T.; Smith, D.B.; Fell, J.B.; Fischer, J.; Spencer, S.R.; Stengel, P.J.; Mohr, P.; Robinson, J.E.; Blake, J.F.; et al. Non-nucleoside inhibitors of HCV polymerase NS5B. Part 2: Synthesis and structure-activity relationships of benzothiazine substituted quinolinediones. Bioorg. Med. Chem. Lett. 2009, 19, 3642-3646.
24. De Vicente, J.; Hendricks, R.T.; Smith, D.B.; Fell, J.B.; Fischer, J.; Spencer, S.R.; Stengel, P.J.; Mohr, P.; Robinson, J.E.; Blake, J.F.; et al. Non-nucleoside inhibitors of HCV polymerase NS5B. Part 3: Synthesis and optimization studies of benzothiazine substituted tetramic acids. Bioorg. Med. Chem. Lett. 2009, 19, 5648-5651.
25. Dragovich, P.S.; Blazel, J.K.; Ellis, D.A.; Han, Q.; Kamran, R.; Kissinger, C.R.; LeBrun, L.A.; Li, L.S.; Murphy, D.E.; Noble, M.; et al. Novel HCV NS5B polymerase inhibitors derived from 4-(1',1'-dioxo-1',4'-dihydro-1'lambda(6)-benzo[1',2',4']thiadiazin-3'-yl)-5-hydroxy-2H-pyridazin-3-ones. Part 5: Exploration of pyridazinones containing 6-amino-substituents. Bioorg. Med. Chem. Lett. 2008, 18, 5635-5639.
26. Gopalsamy, A.; Chopra, R.; Lim, K.; Ciszewski, G.; Shi, M.; Curran, K.J.; Sukits, S.F.; Svenson, K.; Bard, J.; Ellingboe, J.W.; et al. Discovery of proline sulfonamides as potent and selective hepatitis C virus NS5b polymerase inhibitors. Evidence for a new NS5b polymerase binding site. J. Med. Chem. 2006, 49, 3052-3055.
27. Li, L.S.; Zhou, Y.; Murphy, D.E.; Stankovic, N.; Zhao, J.; Dragovich, P.S.; Bertolini, T.; Sun, Z.; Ayida, B.; Tran, C.V.; et al. Novel HCV NS5B polymerase inhibitors derived from 4-(1',1'-dioxo-1',4'-dihydro-1'lambda(6)-benzo[1',2',4']thiadiazin-3'-yl)-5-hydroxy-2H-pyridazin-3-ones. Part 3: Further optimization of the 2-, 6-, and 7'-substituents and initial pharmacokinetic assessments. Bioorg. Med. Chem. Lett. 2008, 18, 3446-3455.
28. Powers, J.P.; Piper, D.E.; Li, Y.; Mayorga, V.; Anzola, J.; Chen, J.M.; Jaen, J.C.; Lee, G.; Liu, J.; Peterson, M.G.; et al. SAR and mode of action of novel non-nucleoside inhibitors of hepatitis C NS5b RNA polymerase. J. Med. Chem. 2006, 49, 1034-1046.
29. Ruebsam, F.; Tran, C.V.; Li, L.S.; Kim, S.H.; Xiang, A.X.; Zhou, Y.; Blazel, J.K.; Sun, Z.; Dragovich, P.S.; Zhao, J.; et al. 5,6-Dihydro-1H-pyridin-2-ones as potent inhibitors of HCV NS5B polymerase. Bioorg. Med. Chem. Lett. 2009, 19, 451-458.
30. Ruebsam, F.; Webber, S.E.; Tran, M.T.; Tran, C.V.; Murphy, D.E.; Zhao, J.; Dragovich, P.S.; Kim, S.H.; Li, L.S.; Zhou, Y.; et al. Pyrrolo[1,2-b]pyridazin-2-ones as potent inhibitors of HCV NS5B polymerase. Bioorg. Med. Chem. Lett. 2008, 18, 3616-3621.
31. Tedesco, R.; Chai, D.; Darcy, M.G.; Dhanak, D.; Fitch, D.M.; Gates, A.; Johnston, V.K.; Keenan, R.M.; Lin-Goerke, J.; Sarisky, R.T.; et al. Synthesis and biological activity of heteroaryl 3-(1,1-dioxo-2H-(1,2,4)-benzothiadizin-3-yl)-4-hydroxy-2(1H)-quinolinone derivatives as hepatitis C virus NS5B polymerase inhibitors. Bioorg. Med. Chem. Lett. 2009, 19, 4354-4358.
32. MOE (The Molecular Operating Environment), version 2010; Chemical Computing Group Inc.: Montreal, Canada, 2010.
33. SONNIA Software, version 4; Molecular Networks GmbH: Erlangen, Germany, 2010.
34. Sadowski, J.; Gasteiger, J. From atoms and bonds to three dimensional atomic coordinates: Automatic model builders. J. Chem. Rev. 1993, 93, 2567-2581.
35. Veber, D.F.; Johnson, S.R.; Cheng, H.Y.; Smith, B.R.; Ward, K.W.; Kopple, K.D. Molecular properties that influence the oral bioavailability of drug candidates. J. Med. Chem. 2002, 45, 2615-2623.
36. Rodgers, J.L.; Nicewander, W.A. Thirteen ways to look at the correlation coefficient. Am. Stat. 1988, 42, 59-66.
37. Cortes, C.; Vapnik, V.N. Support-vector networks. Mach. Learn. 1995, 20, 273-297.
38. Chang, C.C.; Lin, C.J. LIBSVM: A library for support vector machine. 2001. Available online: http://www.csie.ntu.edu.tw/~cjlin/libsvm (accessed on 22 March 2012).