QSAR analysis of poliovirus inhibition by dual combinations of antivirals

Structural Chemistry

Volumn 24, Issue 5, 2013, Pages 1665-1679

  Muratov, E N ^a,b   Varlamova, E V ^a   Artemenko, A G ^a   Polishchuk, P G ^a   Nikolaeva Glomb, L ^c   Galabov, A S ^c   Kuz'Min, V E ^a  

^a A V BOGATSKY PHYSICO CHEMICAL INSTITUTE   (Ukraine)

^b UNC Hamner Institute for Drug Safety Sciences   (United States)

^c INSTITUTE OF MICROBIOLOGY   (Bulgaria)

Author keywords

Dual combinations; Mixture descriptors; Poliovirus; SiRMS

Indexed keywords

HUMAN POLIOVIRUS 1; PICORNAVIRIDAE; POLIOVIRUS;

EID: 84885173417     PISSN: 10400400     EISSN: None     Source Type: Journal    
DOI: 10.1007/s11224-012-0195-8     Document Type: Article

References (77)

1. Prado-Pradoa FJ, Borgesa F, Uriarte E, Perez-Montoto LG, Gonzalez-Díaz H (2009) Multi-target spectral moment: QSAR for antiviral drugs vs. different viral species. Anal Chim Acta 651:159-164
2. Binford SL, Maldonado F, Brothers MA, Weady PT, Zalman LS, Meador JW III, Matthews DA, Patick AK (2005) Conservation of amino acids in human rhinovirus 3C protease correlates with broad-spectrum antiviral activity of rupintrivir, a novel human rhinovirus 3C protease inhibitor. Antimicrob Agents Chemother 49:619-626
3. Conti C, Mastromarino P, Goldoni P, Portalone G, Desideri N (2005) Synthesis and anti-rhinovirus properties of fluoro-substituted flavonoids. Antivir Chem Chemother 16(4):267-276
4. Cutri CC, Garozzo A, Siracusa MA, Castro A, Tempera G, Sarva MC, Guerrera F (2002) Synthesis of new 3-methylthio-5-aryl-4-isothiazolecarbonitriles with broad antiviral spectrum. Antivir Res 55:357-368
5. Diana GD, Cutcliffe D, Oglesby RC, Otto MJ, Mallamo JP, Akullian V, McKinlay MA (1989) Synthesis and structure-activity studies of some disubstituted phenylisoxazoles against human picornavirus. J Med Chem 32:450-455
6. Dragovich PS, Prins TJ, Zhou R, Brown EL, Maldonado FC, Fuhrman SA, Zalman LS, Tuntland T, Lee CA, Patick AK, Matthews DA, Hendrickson TF, Kosa MB, Liu B, Batugo MR, Gleeson JP, Sakata SK, Chen L, Guzman MC, Meador III 3rd, Ferre RA, Worland ST (2002) Structure-based design, synthesis, and biological evaluation of irreversible human rhinovirus 3C protease inhibitors. 6. Structure-activity studies of orally bioavailable, 2-pyridone-containing peptidomimetics. J Med Chem 45:1607-1623
7. Gaudernak E, Seipelt J, Triendl A, Grassauer A, Kuechler E (2002) Antiviral effects of pyrrolidine dithiocarbamate on human rhinoviruses. J Virol 76:6004-6015
8. Kaiser L, Crump CE, Hayden FG (2000) In vitro activity of pleconaril and AG7088 against selected serotypes and clinical isolates of human rhinoviruses. Antivir Res 47:215-220
9. Muratov EN, Artemenko AG, Kuz'min VE, Lozitsky VP, Fedchuk AS, Lozitska RN, Boschenko YA, Gridina TL (2005) Investigation of anti-influenza activity using hierarchic QSAR technology on the base of simplex representation of molecular structure. Antivir Res 65(3):A62-A63
10. Paul JR (1971) A history of poliomyelitis (Yale studies in the history of science and medicine). Yale University Press, New Haven, CT
11. Kew O, Sutter R, de Gourville E, Dowdle W, Pallansch M (2005) Vaccine-derived polioviruses and the endgame strategy for global polio eradication. Annu Rev Microbiol 59:587-635
12. Melnick JL (1990) Poliomyelitis. In: Warren KS, Mahmoud AAF (eds) Tropical and geographical medicine. McGraw-Hill, New York, pp 558-576
13. Atkinson W, Hamborsky J, McIntyre L, Wolfe S (2006) Epidemiology and prevention of vaccine-preventable diseases ("Pink Book"), 9th edn. Public Health Foundation, Washington, DC
14. Cohen JI (2004) Enteroviruses and reoviruses, Chap 175. In: Kasper DL, Braunwald E, Fauci A, Hauser S, Longo D, Jameson JL (eds) Harrison's principles of internal medicine, 16th edn. McGraw-Hill, New York, p 1144
15. Ryan KJ, Ray CG (2004) Sherris medical microbiology: an introduction to infectious diseases, 4th edn. McGraw Hill, New York
16. Katz SL, Gershon AA, Krugman S, Hotez PJ (2004) Krugman's infectious diseases of children. Mosby, St. Louis
17. Ohri LK, Jonathan GM (1999) Polio: will we soon vanquish an old enemy? Drug Benefit Trends 11(6):41-54
18. Nikolaeva L, Galabov AS (1999) In vitro inhibitory effects of dual combinatios of picornavirus replication inhibitors. Acta Virol 43:303-311
19. Ooms F (2000) Molecular modeling and computer aided drug design. examples of their applications in medicinal chemistry. Curr Med Chem 7(2):141-158
20. Thomas G (2008) Medicinal chemistry: an introduction. Wiley, New York
21. Bailey TR, Diana GD, Kowalczyk PJ, Akullian V, Eissenstat MA, Cutcliffe D, Mallamo JP, Carabateas PM, Pevear DC (1992) Antirhinoviral activity of heterocyclic analogs of Win 54954. J Med Chem 35:4628-4633
22. Jenssen H, Gutteberg TJ, Lejon T (2005) Modelling of anti-HSV activity of lactoferricin analogues using amino acid descriptors. J Pept Sci 11(2):97-103
23. Kuz'min VE, Artemenko AG, Lozitsky VP, Muratov EN, Fedtchouk AS, Dyachenko NS, Nosach LN, Gridina TL, Shitikova LI, Mudrik LM, Mescheriakov AK, Chelombitko VA, Zheltvay AI, Vanden Eynde J-J (2002) The analysis of structure - anticancer and antiviral activity relationships for macrocyclic pyridinophanes and their analogues on the basis of 4D QSAR models (simplex representation of molecular structure). Acta Biochim Polon 49:157-168
24. Muratov EN, Varlamova EV, Artemenko AG, Kuz'min VE, Makarov VA, Riabova OB, Wutzler P, Schmidtke M (2011) QSAR analysis of [(biphenyloxy)propyl] isoxazoles: agents against coxsackievirus B3. Future Med Chem 3:31-43
25. Verma RP, Hansch C (2007) Understanding human rhinovirus infections in terms of QSAR. Virology 359(1):152-161
26. Tropsha A, Golbraikh A (2007) Predictive QSAR modeling workflow model applicability domains and virtual screening. Curr Pharm Des 13:3494-3504
27. Artemenko AG, Muratov EN, Atamanyuk DV, Kuz'min VE, Hromov AI, Kutsyk RV, Lesyk RB (2009) QSAR analysis of antimicrobial activity of 4-thiazolidone derivatives. QSAR Comb Sci 29:194-205
28. Fourches D, Barnes JC, Day NC, Bradley P, Reed JZ, Tropsha A (2010) Chemoinformatics analysis of assertions describing drug-induced liver injury in different species. Chem Res Toxicol 23:171-183
29. Kubinyi H (1990) Quantitative structure-activity relationships (QSAR) and molecular modeling in cancer research. J Cancer Res Clin Oncol 116:529-537
30. Fourches D, Muratov EN, 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
31. Muratov EN, Artemenko AG, Varlamova EV, Polischuk PG, Lozitsky VP, Fedtchuk AS, Lozitska RN, Gridina TL, Koroleva LS, Sil'nikov VN, Galabov AS, Makarov VA, Riabova OB, Wutzler P, Schmidtke M, Kuz'min VE (2010) Per aspera ad astra: application of simplex QSAR approach in antiviral research. Future Med Chem 2:1205-1226
32. Lin Z, Yu H, Wei D, Wang G, Feng J, Wang L (2002) Prediction of mixture toxicity with its total hydrophobicity. Chemosphere 46:305-310
33. Wei DB, Zhai LH, Hu H-Y (2004) QSAR-based toxicity classification and prediction for single and mixed aromatic compounds. SAR QSAR Environ Res 15(3):207-216
34. Wang C, Lu G, Tang Z, Guo X (2008) Quantitative structure-activity relationships for joint toxicity of substituted phenols and anilines to Scenedesmus obliquus. J Environ Sci 20:115-119
35. Lin Z, Yin K, Shi P, Wang L, Yu H (2003) Development of QSARs for predicting the joint effects between cyanogenic toxicants and aldehydes. Chem Res Toxicol 16:1365-1371
36. Lin Z, Zhong P, Yin K, Wang L, Yu H (2003) Quantification of joint effect for hydrogen bond and development of QSARs for predicting mixture toxicity. Chemosphere 52:1199-1208
37. Zhang L, Zhou P, Yang F, Wang Z (2007) Computer-based QSARs for predicting mixture toxicity of benzene and its derivatives. Chemosphere 67:396-401
38. Yu H, Lin Z, Feng J, Xu T, Wang L (2001) Development of quantative structure-activity relationships in toxicity prediction of complex mixtures. Acta Pharmacol Sin 22(1):45-49
39. http://www.gaussian.com/.
40. Altenburger R, Nendza M, Schuurmann G (2003) Mixture toxicity and its modeling by quantitative structure-activity relationships. Environ Toxicol Chem 22(8):1900-1915
41. Muratov EN, Varlamova EV, Artemenko AG, Polishchuk PG, Kuz'min VE (2012) Existing and developing approaches for QSAR analysis of mixtures. Mol Inf 31:202-221
42. Tichy M, Cikrt M, Roth Z, Rucki M (1998) QSAR analysis in mixture toxicity assessment. SAR QSAR Environ Res 9:155-169
43. Kuz'min VE, Artemenko AG, Muratov EN (2008) Hierarchical QSAR technology on the base of Simplex representation of molecular structure. J Comput Aid Mol Des 22:403-421
44. Kuz'min VE, Muratov EN, Artemenko AG, Gorb LG, Qasim M, Leszczynski J (2008) The effects of characteristics of substituents on toxicity of the nitroaromatics: HiT QSAR study. J Comp Aid Mol Des 22:747-759
45. Kuz'min VE, Muratov EN, Artemenko AG, Gorb LG, Qasim M, Leszczynski J (2008) The effect of nitroaromatics' composition on their toxicity in vivo: novel, efficient non-additive 1D QSAR analysis. Chemosphere 72:1373-1380
46. Polishchuk PG, Muratov EN, Artemenko AG, Kolumbin OG, Muratov NN, Kuz'min VE (2009) Application of random forest approach to QSAR prediction of aquatic toxicity. J Chem Inf Model 49:2481-2488
47. Artemenko AG, Muratov EN, Kuz'min VE, Kovdienko NA, Hromov AI, Makarov VA, Riabova OB, Wutzler P, Schmidtke M (2007) Identification of individual structural fragments of N,N′-(bis-5-nitropyrimidyl)dispirotripiperazine derivatives for cytotoxicity and antiherpetic activity allows the prediction of new highly active compounds. J Antimicrob Chemother 60(1):68-77
48. Kuz'min VE, Artemenko AG, Lozitska RN, Fedtchouk AS, Lozitsky VP, Muratov EN, Mescheriakov AK (2005) Investigation of anticancer activity of macrocyclic Schiff bases by means of 4D-QSAR based on simplex representation of molecular structure. SAR QSAR Environ Res 16(3):219-230
49. Kuz'min VE, Artemenko AG, Muratov EN, Volineckaya IL, Makarov VA, Riabova OB, Wutzler P, Schmidtke M (2007) Quantitative structure-activity relationship studies of [(biphenyloxy)propyl]isoxazole derivatives - human rhinovirus 2 replication inhibitors. J Med Chem 50:4205-4213
50. Heinz BA, Vance LM (1995) The antiviral compound enviroxime targets the 3A coding region of rhinovirus and poliovirus. J Virol 69:4189-4197
51. Heinz BA, Vance LM (1996) Sequence determinants of 3A-mediated resistance to enviroxime in rhinovirus and enteroviruses. Pharm Ther 10:431-460
52. Zeichhardt H, Otto MJ, McKinlay MA, Willingmann P, Habermehl KO (1987) Inhibition of poliovirus uncoating by disoxaril (WIN 51 711). Virology 160:281-285
53. Eggers HJ, Resenwirth B (1988) Isolation and characterization of an arildone-resistant poliovirus 2 mutant with an altered capsid protein VP1. Antivir Res 9:23-36
54. Lonberg-Holm K, Gosser LB, Kauer JC (1975) Early alteration of poliovirus in infected cells and its specific inhibition. J Gen Virol 27:329-342
55. Baltera JFJ, Tershak DR (1989) Guanidine-resistant mutants of poliovirus have distinct mutations in polypeptide 2C. J Virol 63:4441-4444
56. Barton DJ, Flanegan JB (1997) Synchronous replication of poliovirus RNA: initiation of negative-strand RNA synthesis requires the guanidine-inhibited activity of protein 2C. J Virol 71:8482-8489
57. Dmitrieva TM, Agol VA (1974) Selective inhibition of the synthesis of the single-stranded RNA of encephalo-myocarditis virus by 2-(α-hydroxybenzyl) benzi-midazole in cell-free system. Arch Ges Virusforsch 45:17-24
58. Galabov AS (1979) Thiourea derivatives as specific inhibitors of picornaviruses. Arzneim-Forsch/Drug Res 29:1863-1868
59. Galabov AS, Dmitrieva TM (1983) Inhibitory effect of N-phenyl-N′-3- hydroxy-phenylthiourea (PTU-23) on the reproduction of encephalomyocarditis virus in Krebs-II cells. Zbl Bakt Hyg I Abt Orig A 254:291-305
60. Galabov AS, Ginevskaya VA, Svitkin YV (1983) Effect of N-phenyI-N′-3-hydroxyphenylthiourea (PTU-23) on the protein synthesis in Krebs-II cells infected with encephalomyocarditis virus. Zbl Bakt Hyg I Abt Orig A 254:306-317
61. Canonico PG (1983) Ribavirin. A review of efficacy, toxicity mechanisms of antiviral activity. In: Hahn FE (ed) Antibiotics, vol 6. Springer, Berlin
62. Crotty S, Cameron CE, Andino R (2001) RNA virus error catastrophe: direct molecular test by using ribavirin. Proc Natl Acad Sci USA 98(12):6895-6900
63. Jolly WL, Perry WB (1973) Estimation of atomic charges by an electronegativity equalization procedure calibration with core binding energies. J Am Chem Soc 95:5442-5450
64. Wang R, Fu Y, Lai L (1997) A new atom-additive method for calculating partition coefficients. J Chem Inf Comput Sci 37:615-621
65. Ioffe BV (1983) Chemistry refractometric methods. Himiya, Leningrad
66. Varnek A, Gaudin C, Marcou G, Baskin I, Pandey A, Tetko I (2009) Inductive transfer of knowledge: application of multi-task learning and feature net approaches to model tissue-air partition coefficients. J Chem Inf Model. doi: 10.1021/ci8002914
67. Rannar S, Lindgren F, Geladi P, Wold S (1994) A PLS kernel algorithm for data sets with many variables and fewer objects. Part 1: theory and algorithm. J Chemometr 8:111-125
68. Hasegawa K, Miyashita Y, Funatsu K (1997) GA strategy for variable selection in QSAR studies: GA-based PLS analysis of calcium channel antagonists. J Chem Inf Comput Sci 37:306-310
69. Lindgren F, Geladi P, Rannar S, Wold S (1994) Interactive variable selection (IVS) for PLS. Part 1: theory and algorithms. J Chemometr 8:349-363
70. Kubinyi H (1996) Evolutionary variable selection in regression and PLS analyses. J Chemometr 10:119-133
71. Artemenko A, Muratov E, Kuz'min V, Muratov N, Varlamova E, Kuz'mina A, Golius A, Gorb L, Hill F, Leszczynski J, Tropsha A (2011) QSAR analysis of nitroaromatics' toxicity in tetrahymena pyriformis: structural factors and possible modes of action. SAR QSAR Environ Res 22:575-601
72. Kubinyi H, Hamprecht FA, Mietzner T (1998) Three-dimensional quantitative similarity-activity relationships (3D QSiAR) from SEAL similarity matrices. J Med Chem 41:2553-2564
73. 2. J Mol Graph Model 20:269-276
74. Tropsha A (2010) Best practices for QSAR model development, validation, and exploitation. Mol Inf 29:476-488
75. DrugBank Database (2011) http://www.drugbank.ca/
76. de Palma AM, Vliegen I, de Clercq E, Neyts J (2008) Selective inhibitors of picornavirus replication. Med Res Rev 28(6):823-884
77. Kuz'min VE, Muratov EN, Artemenko AG, Varlamova EV, Gorb LG, Wang J, Leszczynski J (2009) Consensus QSAR modeling of phosphor-containing chiral AChE inhibitors. QSAR Comb Sci 28:664-677