QSAR study of H1N1 neuraminidase inhibitors from influenza a virus

Letters in Drug Design and Discovery

Volumn 11, Issue 4, 2014, Pages 420-427

  Worachartcheewan, Apilak ^a   Nantasenamat, Chanin ^a   Isarankura Na Ayudhya, Chartchalerm ^a   Prachayasittikul, Virapong ^a  

^a MAHIDOL UNIVERSITY   (Thailand)

Author keywords

CORAL; Data mining; Influenza virus; Neuraminidase inhibitors; QSAR; SMILES

Indexed keywords

SIALIDASE INHIBITOR; VIRUS SIALIDASE;

ANTIVIRAL ACTIVITY; ARTICLE; CHEMICAL STRUCTURE; COMPUTER PROGRAM; DRUG DESIGN; DRUG TARGETING; ENZYME INHIBITION; IC 50; INFLUENZA VIRUS A H1N1; MODEL; PRIORITY JOURNAL; QUANTITATIVE STRUCTURE ACTIVITY RELATION; STATISTICAL PARAMETERS;

EID: 84898733194     PISSN: 15701808     EISSN: 1875628X     Source Type: Journal    
DOI: 10.2174/15701808113106660085     Document Type: Article

References (51)

1. Girard, M.P.; Tam, J.S.; Assossou, O.M.; Kieny, M.P. The 2009 A (H1N1) influenza virus pandemic: A review. Vaccine, 2010, 28(31), 4895-4902.
2. Ligon, B.L. Avian influenza virus H5N1: a review of its history and information regarding its potential to cause the next pandemic. Semin. Pediatr. Infect. Dis., 2005, 16(4), 326-335.
3. Rajagopal, S.; Treanor, J. Pandemic (avian) influenza. Semin. Respir. Crit. Care Med., 2007, 28(2), 159-170.
4. Tamura, S.-I.; Kurata, T. Defense mechanisms against influenza virus infection in the respiratory tract mucosa. Jpn. J. Infect. Dis., 2004, 57(6), 236-247.
5. Taubenberger, J.K.; Morens, D.M. The pathology of influenza virus infections. Annu. Rev. Pathol., 2008, 3, 499-522.
6. Moscona, A. Neuraminidase inhibitors for influenza. N. Eng. J. Med., 2005, 353(13), 1363-1373.
7. Ison, M.G. Antivirals and resistance: influenza virus. Curr. Opin. Virol., 2011, 1(6), 563-573.
8. McKimm-Breschkin, J.L. Resistance of influenza viruses to neuraminidase inhibitors-a review. Antiviral Res., 2000, 47(1), 1-17.
9. van der Vries, E.; Schutten, M.; Boucher, C.A. The potential for multidrug-resistant influenza. Curr. Opin. Infect. Dis., 2011, 24(6), 599-604.
10. Yan, S.; Wu, G. Prediction of mutation positions in H5N1 neuraminidases from influenza A virus by means of neural network. Ann. Biomed. Eng., 2010, 38(3), 984-992.
11. Abu Hammad, A.M.; Taha, M.O. Pharmacophore modeling, quantitative structure-activity relationship analysis, and shapecomplemented in silico screening allow access to novel influenza neuraminidase inhibitors. J. Chem. Inf. Model., 2009, 49(4), 978-996.
12. Du, Q.S.; Huang, R.B.; Wei, Y.T.; Pang, Z.W.; Du, L.Q.; Chou, K.C. Fragment-based quantitative structure-activity relationship (FB-QSAR) for fragment-based drug design. J. Comput. Chem., 2009, 30(2), 295-304.
13. Stoll, V.; Stewart, K.D.; Maring, C.J.; Muchmore, S.; Giranda, V.; Gu, Y.G.; Wang, G.; Chen, Y.; Sun, M.; Zhao, C.; Kennedy, A. L.; Madigan, D.L.; Xu, Y.; Saldivar, A.; Kati, W.; Laver, G.; Sowin, T.; Sham, H.L.; Greer, J.; Kempf, D. Influenza neuraminidase inhibitors: structure-based design of a novel inhibitor series. Biochemistry, 2003, 42(3), 718-727.
14. Zhang, J.; Pan, X.; Wang, C.; Wang, F.; Li, P.; Xu, W.; He, L. Pharmacophore modeling, 3D-QSAR studies, and in-silico ADME prediction of pyrrolidine derivatives as neuraminidase inhibitors. Chem. Biol. Drug Des., 2012, 79(3), 353-359.
15. Lü, W.J.; Chen, Y.L.; Ma, W.P.; Zhang, X.Y.; Luan, F.; Liu, M.C.; Chen, X.G.; Hu, Z.D. QSAR study of neuraminidase inhibitors based on heuristic method and radial basis function network. Eur. J. Med. Chem., 2008, 43(3), 569-576.
16. Mercader, A.G.; Pomilio, A.B. QSAR study of flavonoids and biflavonoids as influenza H1N1 virus neuraminidase inhibitors. Eur. J. Med. Chem., 2010, 45(5), 1724-1730.
17. Verma, R.P.; Hansch, C.A. QSAR study on influenza neuraminidase inhibitors. Bioorg. Med. Chem., 2006, 14(4), 982-996.
18. Yi, X.; Guo, Z.; Chu, F.M. Study on molecular mechanism and 3DQSAR of influenza neuraminidase inhibitors. Bioorg. Med. Chem., 2003, 11(7), 1465-1474.
19. Zhang, J.; Yu, K.; Zhu, W.; Jiang, H. Neuraminidase pharmacophore model derived from diverse classes of inhibitors. Bioorg. Med. Chem. Lett., 2006, 16(11), 3009-3014.
20. Zheng, M.; Yu, K.; Liu, H.; Luo, X.; Chen, K.; Zhu, W.; Jiang, H. QSAR analyses on avian influenza virus neuraminidase inhibitors using CoMFA, CoMSIA, and HQSAR. J. Comput. Aided Mol. Des., 2006, 20(9), 549-566.
21. Zhang, Q.; Yang, J.; Liang, K.; Feng, L.; Li, S.; Wan, J.; Xu, X.; Yang, G.; Liu, D.; Yang, S. Binding interaction analysis of the active site and its inhibitors for neuraminidase (N1 subtype) of human influenza virus by the integration of molecular docking, FMO calculation and 3D-QSAR CoMFA modeling. J. Chem. Inf. Model., 2008, 48(9), 1802-1812.
22. Nantasenamat, C.; Isarankura-Na-Ayudhya, C.; Naenna, T.; Prachayasittikul, V. A practical overview of quantitative structureactivity relationship. EXCLI J. 2009, 8, 74-88.
23. Nantasenamat, C.; Isarankura-Na-Ayudhya, C.; Prachayasittikul, V. Advances in computational methods to predict the biological activity of compounds. Expert Opin. Drug Discov., 2010, 5(7), 633-654.
24. Toropova, A.P.; Toropov, A.A.; Benfenati, E.; Gini, G.; Leszczynska, D.; Leszczynski, J. CORAL: quantitative structure-activity relationship models for estimating toxicity of organic compounds in rats. J. Comput. Chem., 2011, 32(12), 2727-2733.
25. Toropova, A.P.; Toropov, A.A.; Lombardo, A.; Roncaglioni, A.; Benfenati, E.; Gini, G. Coral: QSAR models for acute toxicity in fathead minnow (Pimephales promelas). J. Comput. Chem., 2012. doi: 10.1002/jcc.22953.
26. Toropova, A.P.; Toropov, A.A.; Benfenati, E.; Gini, G. QSAR models for toxicity of organic substances to Daphnia magna built up by using the CORAL freeware. Chem. Biol. Drug Des., 2012, 79(3), 332-338.
27. Toropov, A.A.; Toropova, A.P.; Benfenati, E. SMILES-based optimal descriptors: QSAR modeling of carcinogenicity by balance of correlations with ideal slopes. Eur. J. Med. Chem., 2010, 45(9), 3581-3587.
28. Toropov, A.A.; Toropova, A.P.; Benfenati, E.; Manganaro, A. QSAR modelling of the toxicity to Tetrahymena pyriformis by balance of correlations. Mol. Divers., 2010, 14(4), 821-827.
29. Toropov, A.A.; Toropova, A.P.; Benfenati, E.; Leszczynska, D.; Leszczynski, J. SMILES-based optimal descriptors: QSAR analysis of fullerene-based HIV-1 PR inhibitors by means of balance of correlations. J. Comput. Chem., 2010, 31(2), 381-392.
30. Benfenati, E.; Toropov, A.A., Toropova, A.P.; Manganaro, A.; Gonella Diaza, R. Coral Software: QSAR for Anticancer Agents. Chem. Biol. Drug Des., 2011, 77(6), 471-476.
31. Mullen, L.M.A.; Duchowicz, P.R.; Castro, E.A. QSAR treatment on a new class of triphenylmethyl-containing compounds as potent anticancer agents. Chemom. Intell. Lab. Syst., 2011, 107(2), 269-275.
32. Toropov, A.A.; Toropova, A.P.; Benfenati, E.; Gini, G.; Leszczynska, D.; Leszczynski, J. SMILES-based QSAR approaches for carcinogenicity and anticancer activity: comparison of correlation weights for identical SMILES attributes. Anticancer Agents Med. Chem., 2011, 11(10), 974-982.
33. Ibezim, E.; Duchowicz, P.R.; Ortiz, E.V.; Castro, E.A. QSAR on aryl-piperazine derivatives with activity on malaria. Chemom. Intell. Lab. Syst., 2012, 110(1), 81-88.
34. Kim, C.U.; Lew, W.; Williams, M.A.; Wu, H.; Zhang, L.; Chen, X.; Escarpe, P.A.; Mendel, D.B.; Laver, W.G.; Stevens, R.C. Structure- activity relationship studies of novel carbocyclic influenza neuraminidase inhibitors. J. Med. Chem., 1998, 41(14), 2451-2460.
35. Chand, P.; Babu, Y.S.; Bantia, S.; Rowland, S.; Dehghani, A.; Kotian, P.L.; Hutchison, T.L.; Ali, S.; Brouillette, W.; El-Kattan, Y.; Lin, T.H. Syntheses and neuraminidase inhibitory activity of multisubstituted cyclopentane amide derivatives. J. Med. Chem., 2004, 47(8), 1919-1929.
36. Chand, P.; Kotian, P.L.; Dehghani, A.; El-Kattan, Y.; Lin, T.H.; Hutchison, T.L.; Babu, Y.S.; Bantia, S.; Elliott, A.J.; Montgomery, J.A. Systematic structure-based design and stereoselective synthesis of novel multisubstituted cyclopentane derivatives with potent antiinfluenza activity. J. Med. Chem., 2001, 44(25), 4379-4392.
37. Wang, G.T.; Chen, Y.; Wang, S.,; Gentles, R.; Sowin, T.; Kati, W.; Muchmore, S.; Giranda, V.; Stewart, K.; Sham, H.; Kempf, D.; Laver, W.G. Design, synthesis, and structural analysis of influenza neuraminidase inhibitors containing pyrrolidine cores. J. Med. Chem., 2011, 44(8), 1192-1201.
38. ACD/ChemSketch Freeware, version 12.00, Advanced Chemistry Development, Inc., Toronto, ON, Canada, Available at: http://www.acdlabs.com/resources/ freeware/chemsketch, Accessed on March 20, 2012.
39. Murumkar, P.R.; Le, L.; Truong, T.N.; Yadav, M.R. Determination of structural requirements of influenza neuraminidase type A inhibitors and binding interaction analysis with the active site of A/H1N1 by 3D-QSAR CoMFA and CoMSIA modeling. Med. Chem. Commun., 2011, 2(8), 710-719.
40. Worachartcheewan, A.; Prachayasittikul, S.; Pingaew, R.; Nantasenamat, C.; Tantimongcolwat, T.; Ruchirawat, S.; Prachayasittikul, V. Antioxidant, cytotoxicity, and QSAR study of 1- adamantylthio derivatives of 3-picoline and phenylpyridines. Med. Chem. Res., 2012, 21(11), 3514-3522.
41. Pingaew, R.; Tongraung, P.; Worachartcheewan, A.; Nantasenamat, C.; Prachayasittikul, S.; Ruchirawat, S.; Prachayasittikul, V. Cytotoxicity and QSAR study of (thio)ureas derived from phenylalkylamines and pyridylalkylamines. Med. Chem. Res., 2013, 22(8), 4016-4029.
42. Worachartcheewan, A.; Nantasenamat, C.; Isarankura-Na- Ayudhya, C.; Prachayasittikul, V. QSAR study of amidino bisbenzimidazole derivatives as potent anti-malarial agents against Plasmodium falciparum. Chem. Pap., 2013, 67(11), 1462-1473.
43. Sawant, R.L.; Bansode, C.A.; Wadekar, J.B. In vitro antiinflammatory potential and QSAR analysis of oxazolo/thiazolo pyrimidine derivatives. Med. Chem. Res., 2013, 22(4), 1884-1892.
44. Golbraikh, A.; Tropsha, A. Beware of q2!. J. Mol. Graph. Model., 2002, 20(4), 269-276.
45. Ojha, P.K.; Mitra, I.; Das, R.N.; Roy, K. Further exploring rm 2 metrics for validation of QSPR models. Chemom. Intell. Lab. Syst., 2011, 107(1), 194-205.
46. Roy, P.P.; Roy, K. On some aspects of variable selection for partial least squares regression models. QSAR Comb. Sci., 2008, 27(3), 302-313.
47. Toropova, A.P.; Toropov, A.A.; Benfenati, E.; Gini, G.; Leszczynska, D.; Leszczynski, J. CORAL: QSAR modeling of toxicity of organic chemicals towards Daphnia magna. Chemom. Intell. Lab. Syst., 2012, 110(1), 177-181.
48. Toropov, A.A.; Toropova, A.P.; Martyanov, S.E.; Benfenati, E.; Gini, G.; Leszczynska, D.; Leszczynski, J. CORAL: Predictions of rate constants of hydroxyl radical reaction using representation of the molecular structure obtained by combination of SMILES and Graph approaches. Chemom. Intell. Lab. Syst., 2012, 112, 65-70.
49. Toropova, A.P.; Toropov, A.A.; Benfenati, E.; Gini, G. QSAR modelling toxicity toward rats of inorganic substances by means of CORAL. Cent. Eur. J. Chem. 2011, 9(1), 75-85.
50. Toropov, A.A.; Toropova, A.P.; Benfenati, E.; Manganaro, A. QSAR modelling of carcinogenicity by balance of correlations. Mol. Divers., 2009, 13(3), 367-733.
51. Toropov, A.A.; Toropova, A.P.; Lombardo, A.; Roncaglioni, A.; Benfenati, E.; Gini, G. CORAL: building up the model for bioconcentration factor and defining it's applicability domain. Eur. J. Med. Chem., 2011, 46(4), 1400-1403.