Consensus QSAR model for identifying novel H5N1 inhibitors

Molecular Diversity

Volumn 16, Issue 3, 2012, Pages 513-524

  Sharma, Nitin ^a   Yap, Chun Wei ^a  

^a NATIONAL UNIVERSITY OF SINGAPORE   (Singapore)

Author keywords

Applicability domain; Consensus model; H5N1; In silico screening; Inhibitors; QSAR

Indexed keywords

ANTIVIRUS AGENT; H5N1 INHIBITOR; OSELTAMIVIR; SIALIDASE; SIALIDASE INHIBITOR; UNCLASSIFIED DRUG;

ACCURACY; ARTICLE; DRUG TARGETING; EXTERNAL VALIDITY; FALSE POSITIVE RESULT; INFLUENZA; INFLUENZA A (H5N1); INFLUENZA VIRUS A H5N1; NONHUMAN; PRIORITY JOURNAL; QUANTITATIVE STRUCTURE ACTIVITY RELATION; SENSITIVITY AND SPECIFICITY;

ANTIVIRAL AGENTS; DRUG EVALUATION, PRECLINICAL; INFLUENZA A VIRUS, H5N1 SUBTYPE; NEURAMINIDASE; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 84869493274     PISSN: 13811991     EISSN: 1573501X     Source Type: Journal    
DOI: 10.1007/s11030-012-9384-z     Document Type: Article

References (57)

1. World Health Organization (2005) Avian influenza and human pandemic influenza, Summary Report. Geneva, Switzerland
2. Chen H, Smith GJD, Zhang SY, Qin K, Wang J, Li KS, Webster RG, Peiris JSM, Guan Y (2005) Avian flu H5N1 virus outbreak in migratory waterfowl. Nature 436:191-192. http://www.nature.com/nature/journal/v436/n7048/suppinfo/ nature03974-S1.html (Pubitemid 41021261)
3. Beigel JH (2005) Avian influenza A (H5N1) infection in humans. New Eng J Med 353:1374-1385 (Pubitemid 41362705)
4. World Health Organization (2009) Pandemic influenza preparedness and response. WHO, Geneva
5. Skehel JJ, Wiley DC (2000) Receptor binding and membrane fusion in virus entry: the influenza hemagglutinin. Annu Rev Biochem 69:531-569. doi:10.1146/annurev.biochem.69.1.531
6. Pinto LH, Lamb RA (2006) The M2 proton channels of influenza A and B viruses. J Biol Chem 281:8997-9000 (Pubitemid 43864610)
7. Schnell JR, Chou JJ (2008) Structure and mechanism of the M2 proton channel of influenza A virus. Nature 451:591-595. http://www.nature.com/nature/ journal/v451/n7178/suppinfo/nature06531-S1.html (Pubitemid 351186272)
8. Gong J, Xu W, Zhang J (2007) Structure and functions of influenza virus neuraminidase. Curr Med Chem 14:113-122 (Pubitemid 46050308)
9. De Clercq E (2006) Antiviral agents active against influenza A viruses. Nat Rev Drug Discov 5:1015-1025 (Pubitemid 44835128)
10. Layne SP, Monto AS, Taubenberger JK (2009) Pandemic influenza: an inconvenient mutation. Science 323:1560-1561
11. Hansch C, Leo A (1995) Exploring QSAR: fundamentals and applications in chemistry and biology. American Chemical Society, Washington, DC
12. Nair PC, Sobhia ME (2008) Quantitative structure activity relationship studies on thiourea analogues as influenza virus neuraminidase inhibitors. Eur J Med Chem 43:293-299. doi:10.1016/j.ejmech.2007.03.020 (Pubitemid 351215598)
13. Du QS, Huang RB, Wei YT, Du LQ, Chou KC (2008) Multiple field three dimensional quantitative structure-activity relationship (MF-3D-QSAR). J Comput Chem 29:211-219. doi:10.1002/jcc. 20776
14. Du QS, Huang RB, Wei YT, Pang ZW, Du LQ, Chou KC (2009) Fragment-based quantitative structure-activity relationship (FB-QSAR) for fragment-based drug design. J Comput Chem 30: 295-304. doi:10.1002/jcc.21056
15. Gramatica P (2007) Principles of QSAR models validation: internal and external. QSAR Combinatorial Sci 26:694-701. doi:10.1002/qsar.200610151 (Pubitemid 46932857)
16. Parker CN, Bajorath J (2006) Towards unified compound screening strategies: a critical evaluation of error sources in experimental and virtual high-throughput screening. QSAR Combinatorial Sci 25:1153-1161. doi:10.1002/qsar.200610069 (Pubitemid 46052452)
17. Han LY, Ma XH, Lin HH, Jia J, Zhu F, Xue Y, Li ZR, Cao ZW, Ji ZL, Chen YZ (2008) A support vector machines approach for virtual screening of active compounds of single and multiple mechanisms from large libraries at an improved hit-rate and enrichment factor. J Mol Graph Model 26:1276-1286. doi:10.1016/j.jmgm. 2007.12.002
18. Smith PW, Sollis SL, Howes PD, Cherry PC, Starkey ID, Cobley KN, Weston H, Scicinski J, Merritt A, Whittington A, Wyatt P, Taylor N, Green D, Bethell R, Madar S, Fenton RJ, Morley PJ, Pateman T, Beresford A (1998) Dihydropyrancarboxamides related to zanamivir: a new series of inhibitors of influenza virus sialidases. 1. Discovery, synthesis, biological activity, and structure-activity relationships of 4-guanidino-and 4-amino-4H-pyran-6- carboxamides. J Med Chem 41:787-797. doi:10.1021/jm970374b (Pubitemid 28146236)
19. Kim CU, Lew W, Williams MA, Wu H, Zhang L, Chen X, Escarpe PA, Mendel DB, Laver WG, Stevens RC (1998) Structure-activity relationship studies of novel carbocyclic influenza neuraminidase inhibitors. J Med Chem 41:2451-2460. doi:10.1021/jm980162u (Pubitemid 28321896)
20. Lew W, Wu H, Mendel DB, Escarpe PA, Chen X, Laver WG, Graves BJ, Kim CU (1998) A new series of C3-aza carbocyclic influenza neuraminidase inhibitors: synthesis and inhibitory activity. Bioorg Med Chem Lett 8:3321-3324. doi:10.1016/s0960-894x(98)00587-3 (Pubitemid 28547065)
21. Lew W, Wu H, Chen X, Graves BJ, Escarpe PA, MacArthur HL, Mendel DB, Kim CU (2000) Carbocyclic influenza neuraminidase inhibitors possessing a C3-cyclic amine side chain: synthesis and inhibitory activity. BioorgMed Chem Lett 10:1257-1260. doi:10.1016/s0960-894x(00)00214-6 (Pubitemid 30345104)
22. Honda T, Masuda T, Yoshida S, Arai M, Kobayashi Y, Yamashita M (2002) Synthesis and anti-influenza virus activity of 4-guanidino-7-substituted Neu5Ac2en derivatives. Bioorg Med Chem Lett 12:1921-1924. doi:10.1016/s0960- 894x(02)00328-1 (Pubitemid 34756449)
23. Honda T, Masuda T, Yoshida S, Arai M, Kaneko S, Yamashita M (2002) Synthesis and anti-influenza virus activity of 7-O-Alkylated derivatives related to zanamivir. Bioorg Med Chem Lett 12:1925-1928. doi:10.1016/s0960-894x(02) 00329-3 (Pubitemid 34756450)
24. Masuda T (2003) Synthesis and anti-influenza evaluation of orally active bicyclic ether derivatives related to zanamivir. Bioorg Med Chem Lett 13:669-673. doi:10.1016/s0960-894x(02)01039-9 (Pubitemid 36298465)
25. SunC, Zhang X, HuangH, Zhou P (2006) Synthesis and evaluation of a new series of substituted acyl(thio)urea and thiadiazolo [2,3-a] pyrimidine derivatives as potent inhibitors of influenza virus neuraminidase. Bioorg Med Chem 14:8574-8581. doi:10.1016/j.bmc.2006.08.034 (Pubitemid 44667533)
26. Hurt AC, Selleck P, Komadina N, Shaw R, Brown L, Barr IG (2007) Susceptibility of highly pathogenic A(H5N1) avian influenza viruses to the neuraminidase inhibitors and adamantanes. Antiviral Res 73:228-231. doi:10.1016/j.antiviral.2006.10.004
27. Shie JJ, Fang JM, Wang SY, Tsai KC, Cheng YSE, Yang AS, Hsiao SC, Su CY, Wong CH (2007) Synthesis of tamiflu and its phosphonate congeners possessing potent anti-influenza activity. J Am Chem Soc 129:11892-11893
28. Abed Y, Nehme B, Baz M, Boivin G (2008) Activity of the neuraminidase inhibitor A-315675 against oseltamivir-resistant influenza neuraminidases of N1 and N2 subtypes. Antiviral Res 77:163-166. doi:10.1016/j.antiviral.2007.08.008
29. Liu AL, Wang HD, Lee SM, Wang YT, Du GH (2008) Structure- activity relationship of flavonoids as influenza virus neuraminidase inhibitors and their in vitro anti-viral activities. Bioorg Med Chem 16:7141-7147. doi:10.1016/j.bmc.2008.06.049
30. Yamashita M, Tomozawa T, Kakuta M, Tokumitsu A, Nasu H, Kubo S (2009) CS-8958, a prodrug of the new neuraminidase inhibitorR-125489, shows long-acting anti-influenza virus activity. Antimicrob Agents Chemother 53:186-192. doi:10.1128/AAC.00333-08
31. Rao JR, Jha AK, Rawal RK, Sharon A, Day CW, Barnard DL, Smee DF, Chu CK (2010) (-)-Carbodine: enantiomeric synthesis and in vitro antiviral activity against various strains of influenza virus including H5N1 (avian influenza) and novel 2009 H1N1 (swine flu). Bioorg Med Chem Lett 20:2601-2604. doi:10.1016/j.bmcl.2010.02.074
32. Wen WH, Wang SY, Tsai KC, Cheng YS, Yang AS, Fang JM, Wong CH (2010) Analogs of zanamivir with modified C4-substituents as the inhibitors against the group-1 neuraminidases of inflenza viruses. Bioorg Med Chem 18:4074-4084. doi:10.1016/j.bmc.2010.04.010
33. Dao TT, Tung BT, Nguyen PH, Thuong PT, Yoo SS, Kim EH, Kim SK, Oh WK (2010) C-methylated flavonoids from cleistocalyx operculatus and their inhibitory effects on novel influenza a (H1N1) neuraminidase. J Nat Prod 73:1636-1642
34. Dao TT, Nguyen PH, Lee HS, Kim E, Park J, Lim SI, Oh WK (2011) Chalcones as novel influenza A (H1N1) neuraminidase inhibitors from Glycyrrhiza inflata. Bioorg Med Chem Lett 21:294-298. doi:10.1016/j.bmcl.2010.11.016
35. Liu Y, Jing F, Xu Y, Xie Y, Shi F, Fang H, Li M, Xu W (2011) Design, synthesis and biological activity of thiazolidine-4-carboxylic acid derivatives as novel influenza neuraminidase inhibitors. Bioorg Med Chem 19:2342-2348. doi:10.1016/j.bmc.2011.019
36. Williams MA, Lew W, Mendel DB, Tai CY, Escarpe PA, Laver WG, Stevens RC, Kim CU (1997) Structure-activity relationships of carbocyclic influenza neuraminidase inhibitors. Bioorg Med Chem Lett 7:1837-1842. doi:10.1016/s0960- 894x(97)00333-8 (Pubitemid 27317799)
37. CambridgeSoft Desktop Software-ChemDraw (Windows/Mac) http://www.cambridgesoft.com/. Accessed 06 Jun 2011
38. Pipeline Pilot http://accelrys.com/products/pipeline-pilot/. Accessed 09 Feb 2011
39. Fourches D, Muratov E, Tropsha A (2010) Trust, but verify: on the importance of chemical structure curation in cheminformatics and QSAR modeling research. J Chem Inf Model 50:1189-1204. doi:10.1021/ci100176x
40. Dearden JC, CroninMTD, Kaiser KLE (2009) How not to develop a quantitative structure-activity or structure-property relationship (QSAR/QSPR). SAR QSAR Environ Res 20:241-266
41. Garozzo A, Timpanaro R, Stivala A, Bisignano G, Castro A (2011) Activity of Melaleuca alternifolia (tea tree) oil on Influenza virus A/PR/8: study on the mechanism of action. Antiviral Res 89:83-88. doi:10.1016/j.antiviral.2010.11. 010
42. Cheng LS, Amaro RE, Xu D, Li WW, Arzberger PW, McCammon JA (2008) Ensemble-based virtual screening reveals potential novel antiviral compounds for avian influenza neuraminidase. J Med Chem 51:3878-3894. doi:10.1021/jm8001197 (Pubitemid 351956517)
43. Yap CW (2011) PaDEL-descriptor: an open source software to calculate molecular descriptors and fingerprints. J Comput Chem 32:1466-1474. doi:10.1002/jcc.21707
44. Tan P-N, Steinbach M, Kumar V (2005) Introduction to data mining. Addison Wesley, Boston
45. VapnikV (1995) The nature of statistical learning theory. Springer, London
46. MOE: Molecular Operating Enviroment. 2011.10 edn. Chemical Computing Group Inc., 1010 Sherbooke St. West, Suite #910, Montreal, QC, Canada, H3A 2R7, 2011
47. Tropsha A, Golbraikh A (2007) Predictive QSAR modeling workflow, model applicability domains, and virtual screening, Curr Pharm Des 13:3494-3504. doi:10.2174/138161207782794257 (Pubitemid 350238939)
48. Weaver S, Gleeson MP (2008) The importance of the domain of applicability in QSAR modeling. J Mol Graph Model 26: 1315-1326. doi:10.1016/j.jmgm.2008.01. 002
49. Jaworska J, Nikolova-Jeliazkova N, Aldenberg T (2005) QSAR applicability domain estimation by projection of the training set in descriptor space: a review. ATLA Altern Lab Anim 33: 445-459 (Pubitemid 41613738)
50. Giorgio Fumera, Fabio Roli, Giacinto G (2000) Reject option with multiple thresholds. Pattern Recogn Soc 33:2099-2101
51. ZINC http://zinc.docking.org/. Accessed 03 Aug 2010
52. Lange JHM, Coolen HKAC, van der Neut MAW, Borst AJM, Stork B, Verveer PC, Kruse CG (2010) Design, synthesis, biological properties, and molecular modeling investigations of novel tacrine derivatives with a combination of acetylcholinesterase inhibition and cannabinoid CB1 receptor antagonism. J Med Chem 53:1338-1346. doi:10.1021/jm901614b
53. Birchall K, Gillet VJ, Harper G, Pickett SD (2008) Evolving interpretable structure-activity relationship models. 2. Using multiobjective optimization to derive multiple models. J Chem Inf Model 48:1558-1570. doi:10.1021/ci800051h
54. Naik P, Santoshi S, Joshi H (2012) Noscapinoids with anti-cancer activity against human acute lymphoblastic leukemia cells (CEM): a three dimensional chemical space pharmacophore modeling and electronic feature analysis. J Mol Model 18:307-318. doi:10.1007/s00894-011-1057-9
55. Song Y, Huang J, Zhou D, Zha H, Giles C (2007) IKNN: Informative K-nearest neighbor pattern classification knowledge discovery in databases: PKDD 2007. In: Kok J, Koronacki J, Lopezde Mantaras R, Matwin S, Mladenic D, Skowron A (eds) Lecture Notes in Computer Science, vol 4702. Springer, Berlin pp 248- 264. doi:10.1007/978-3-540-74976-9-25
56. Hill T, Lewicki P (2006) Statistics: Methods and Applications. A Comprehensive Reference for Science, Industry, and Data Mining. Statsoft, Tulsa, OK, USA
57. Tong W, Xie Q, Hong H, Shi L, Fang H, Perkins R (2004) Assessment of prediction confidence and domain extrapolation of two structure-activity relationship models for predicting estrogen receptor binding activity. Environ Health Perspect 112: 1249-1254 (Pubitemid 39199565)