Discovery of new scaffolds for rational design of HCV NS5B polymerase inhibitors

European Journal of Medicinal Chemistry

Volumn 58, Issue , 2012, Pages 258-264

  Golub, Andriy G ^a   Gurukumar, K R ^b   Basu, Amartya ^b   Bdzhola, Volodymyr G ^a   Bilokin, Yaroslav ^c   Yarmoluk, Sergiy M ^a,c   Lee, Jin Ching ^d   Talele, Tanaji T ^e   Nichols, Daniel B ^b   Kaushik Basu, Neerja ^b  

^a INSTITUTE OF MOLECULAR BIOLOGY AND GENETICS   (Ukraine)

^b RUTGERS NEW JERSEY MEDICAL SCHOOL   (United States)

^c Otava Ltd   (Ukraine)

^d KAOHSIUNG MEDICAL UNIVERSITY   (Taiwan)

^e ST JOHN'S UNIVERSITY   (United States)

Author keywords

Hepatitis C virus; NS5B inhibitors; NS5B polymerase; Thumb pocket; Virtual screening

Indexed keywords

2 (QUINAZOLIN 4 YL HYDRAZONO)PROPIONIC ACID; 2 [ N' ( 3 BROMO 4 HYDROXY 5 METHOXYBENZYLIDENE)HYDRAZINO]BENZOIC ACID; 2 HYDROXY 4 ( 5 OXO 6 PHENYL 4,5 DIHYDRO[1,2,4]TRIAZIN 3 YLAMINO)BENZOIC ACID; 3 [ 1 ( 2 CARBOXYETHYL) 3 ( 4 FLUOROPHENYL) 1H PYRAZOL 4 YL] 2 CYANOACRYLIC ACID ETHYL ESTER; 3 BENZENESULFONYL 1 [ 4 ( 3 BENZENESULFONYLPROPIONYL)PIPERAZIN 1 YL]PROPAN 1 ONE; 3,3' [( 3,4 DICHLOROPHENYL)METHYLENE]BIS( 4 HYDROXY 6 METHYL 2H PYRAN 2 ONE); 4 ( 4 METHYL 1,1,3 TRIOXO 1 LAMBDA 6 ISOTHIAZOLIDIN 2 YL) N QUINOLIN 8 YL BENZENESULFONAMIDE; 7 [ 4 ( 2,4 DIFLUOROBENZOYL)PIPERAZIN 1 CARBONYL] 5 METHYL 2 PHENYL 2,5 DIHYDROPYRAZOLO[4,3 C]PYRIDIN 3 ONE; ANTIVIRUS AGENT; BENZOIC ACID DERIVATIVE; BENZOISOQUINOLINE; DIHYDROPYRANONE; MOLECULAR SCAFFOLD; NONNUCLEOSIDE REVERSE TRANSCRIPTASE INHIBITOR; NONSTRUCTURAL PROTEIN 5B; NS5B POLYMERASE INHIBITOR; P 1297082; P 1588489; P 1888291; P 7020351141; P 7020431675; P 7020527349; P 7117160121; P 7215300002; PYRIDINE DERIVATIVE; THIAZOLE DERIVATIVE; THIAZOLONE; UNCLASSIFIED DRUG;

ALLOSTERISM; ANIMAL CELL; ANTIVIRAL ACTIVITY; ARTICLE; BINDING SITE; CELL LINE; CONTROLLED STUDY; CYTOTOXICITY; DATA BASE; DRUG BINDING; DRUG DESIGN; DRUG POTENCY; DRUG SCREENING; ENZYME ACTIVITY; ENZYME INHIBITION; HEPATITIS C VIRUS; IC 50; IN VITRO STUDY; MINIMUM INHIBITORY CONCENTRATION; MOLECULAR LIBRARY; MUTANT; NONHUMAN; REPORTER GENE; VIRUS STRAIN;

DOSE-RESPONSE RELATIONSHIP, DRUG; DRUG DISCOVERY; ENZYME INHIBITORS; HIGH-THROUGHPUT SCREENING ASSAYS; HYDRAZINES; MODELS, MOLECULAR; MOLECULAR STRUCTURE; QUINAZOLINONES; STRUCTURE-ACTIVITY RELATIONSHIP; VIRAL NONSTRUCTURAL PROTEINS;

EID: 84868239146     PISSN: 02235234     EISSN: 17683254     Source Type: Journal    
DOI: 10.1016/j.ejmech.2012.09.010     Document Type: Article

References (47)

1. L.B. Seeff Dilemma of the natural history of hepatitis C J. Gastroenterol. Hepatol. 14 1999 199 201
2. C.W. Shepard, L. Finelli, and M.J. Alter Global epidemiology of hepatitis C virus infection Lancet Infect. Dis. 5 2005 558 567
3. J.F. Dillon Hepatitis C: what is the best treatment? J. Viral Hepat. 11 Suppl. 1 2004 23 27
4. Z.J. Ni, and A.S. Wagman Progress and development of small molecule HCV antivirals Curr. Opin. Drug Discovery Dev. 7 2004 446 459
5. M. Cornberg, H. Wedemeyer, and M.P. Manns Treatment of chronic hepatitis C with PEGylated interferon and ribavirin Curr. Gastroenterol. Rep. 4 2002 23 30
6. O. Reichard, G. Norkrans, A. Fryden, J.H. Braconier, A. Sonnerborg, and O. Weiland Randomised, double-blind, placebo-controlled trial of interferon alpha-2b with and without ribavirin for chronic hepatitis C. the Swedish study group Lancet 351 1998 83 87
7. P. Farci, I. Quinti, S. Farci, H.J. Alter, R. Strazzera, E. Palomba, A. Coiana, D. Cao, A.M. Casadei, R. Ledda, R. Iorio, A. Vegnente, G. Diaz, and P.A. Tovo Evolution of hepatitis C viral quasispecies and hepatic injury in perinatally infected children followed prospectively Proc. Natl. Acad. Sci. U. S. A 103 2006 8475 8480
8. P. Ferenci Pegylated interferon plus ribavirin for chronic hepatitis C: the role of combination therapy today, tomorrow and in the future Minerva Gastroenterologica E Dietologica 52 2006 157 174
9. C. Rice Perspective: miles to go before we sleep Nature 474 2011 S8
10. C. Sheridan New Merck and Vertex drugs raise standard of care in hepatitis C Nat. Biotechnol. 29 2011 553 554
11. K. Garber Hepatitis C: move over interferon Nat. Biotechnol. 29 2011 963 966
12. Q.L. Choo, G. Kuo, A.J. Weiner, L.R. Overby, D.W. Bradley, and M. Houghton Isolation of a cDNA clone derived from a blood-borne non-A, non-B viral hepatitis genome Science 244 1989 359 362
13. K.E. Reed, and C.M. Rice Overview of hepatitis C virus genome structure, polyprotein processing, and protein properties Curr. Top. Microbiol. Immunol. 242 2000 55 84
14. Y. Tanji, M. Hijikata, Y. Hirowatari, and K. Shimotohno Hepatitis C virus polyprotein processing: kinetics and mutagenic analysis of serine proteinase-dependent cleavage J. Virol. 68 1994 8418 8422
15. J. Vermehren, and C. Sarrazin New HCV therapies on the horizon Clin. Microbiol. Infect. 17 2011 122 134
16. S.E. Behrens, L. Tomei, and R. De Francesco Identification and properties of the RNA-dependent RNA polymerase of hepatitis C virus EMBO J. 15 1996 12 22
17. D. Moradpour, V. Brass, E. Bieck, P. Friebe, R. Gosert, H.E. Blum, R. Bartenschlager, F. Penin, and V. Lohmann Membrane association of the RNA-dependent RNA polymerase is essential for hepatitis C virus RNA replication J. Virol. 78 2004 13278 13284
18. M.L. Barreca, N. Iraci, G. Manfroni, and V. Cecchetti Allosteric inhibition of the hepatitis C virus NS5B polymerase: in silico strategies for drug discovery and development Future Med. Chem. 3 2011 1027 1055
19. H. Ago, T. Adachi, A. Yoshida, M. Yamamoto, N. Habuka, K. Yatsunami, and M. Miyano Crystal structure of the RNA-dependent RNA polymerase of hepatitis C virus Structure 7 1999 1417 1426
20. S. Bressanelli, L. Tomei, F.A. Rey, and R. De Francesco Structural analysis of the hepatitis C virus RNA polymerase in complex with ribonucleotides J. Virol. 76 2002 3482 3492
21. S. Bressanelli, L. Tomei, A. Roussel, I. Incitti, R.L. Vitale, M. Mathieu, R. De Francesco, and F.A. Rey Crystal structure of the RNA-dependent RNA polymerase of hepatitis C virus Proc. Natl. Acad. Sci. U. S. A 96 1999 13034 13039
22. C.A. Lesburg, M.B. Cable, E. Ferrari, Z. Hong, A.F. Mannarino, and P.C. Weber Crystal structure of the RNA-dependent RNA polymerase from hepatitis C virus reveals a fully encircled active site Nat. Struct. Biol. 6 1999 937 943
23. T.T. Talele, P. Arora, S.S. Kulkarni, M.R. Patel, S. Singh, M. Chudayeu, and N. Kaushik-Basu Structure-based virtual screening, synthesis and SAR of novel inhibitors of hepatitis C virus NS5B polymerase Bioorg. Med. Chem. 18 2010 4630 4638
24. D.B. Nichols, G. Fournet, K.R. Gurukumar, A. Basu, J.C. Lee, N. Sakamoto, F. Kozielskie, I. Musmuca, B. Joseph, R. Ragno, and N. Kaushik-Basua Inhibition of hepatitis C virus NS5B polymerase by S-Trityl-L-Cysteine derivatives Eur. J. Med. Chem. 49 2012 191 199
25. I. Musmuca, A. Caroli, A. Mai, N. Kaushik-Basu, P. Arora, and R. Ragno Combining 3-D quantitative structure-activity relationship with ligand based and structure based alignment procedures for in silico screening of new hepatitis C virus NS5B polymerase inhibitors J. Chem. Inf. Model. 50 2010 662 676
26. S. Yan, T. Appleby, G. Larson, J.Z. Wu, R.K. Hamatake, Z. Hong, and N. Yao Thiazolone-acylsulfonamides as novel HCV NS5B polymerase allosteric inhibitors: convergence of structure-based drug design and X-ray crystallographic study Bioorg. Med. Chem. Lett. 17 2007 1991 1995
27. R.A. Love, H.E. Parge, X. Yu, M.J. Hickey, W. Diehl, J. Gao, H. Wriggers, A. Ekker, L. Wang, J.A. Thomson, P.S. Dragovich, and S.A. Fuhrman Crystallographic identification of a noncompetitive inhibitor binding site on the hepatitis C virus NS5B RNA polymerase enzyme J. Virol. 77 2003 7575 7581
28. M. Wang, K.K. Ng, M.M. Cherney, L. Chan, C.G. Yannopoulos, J. Bedard, N. Morin, N. Nguyen-Ba, M.H. Alaoui-Ismaili, R.C. Bethell, and M.N. James Non-nucleoside analogue inhibitors bind to an allosteric site on HCV NS5B polymerase. Crystal structures and mechanism of inhibition J. Biol. Chem. 278 2003 9489 9495
29. C.A. Lipinski, F. Lombardo, B.W. Dominy, and P.J. Feeney Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings Adv. Drug Delivery Rev. 46 2001 3 26
30. S. Yan, T. Appleby, G. Larson, J.Z. Wu, R. Hamatake, Z. Hong, and N. Yao Structure-based design of a novel thiazolone scaffold as HCV NS5B polymerase allosteric inhibitors Bioorg. Med. Chem. Lett. 16 2006 5888 5891
31. B.K. Biswal, M. Wang, M.M. Cherney, L. Chan, C.G. Yannopoulos, D. Bilimoria, J. Bedard, and M.N. James Non-nucleoside inhibitors binding to hepatitis C virus NS5B polymerase reveal a novel mechanism of inhibition J. Mol. Biol. 361 2006 33 45
32. J.M. Ontoria, E.H. Rydberg, S. Di Marco, L. Tomei, B. Attenni, S. Malancona, J.I. Martin Hernando, N. Gennari, U. Koch, F. Narjes, M. Rowley, V. Summa, S.S. Carroll, D.B. Olsen, R. De Francesco, S. Altamura, G. Migliaccio, and A. Carfi 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. 52 2009 5217 5227
33. N. Kaushik-Basu, A. Bopda-Waffo, T.T. Talele, A. Basu, Y. Chen, and S.G. Kucukguzel 4-Thiazolidinones: a novel class of hepatitis C virus NS5B polymerase inhibitors Front. Biosci. 13 2008 3857 3868
34. Y. Chen, A. Bopda-Waffo, A. Basu, R. Krishnan, E. Silberstein, D.R. Taylor, T.T. Talele, P. Arora, and N. Kaushik-Basu Characterization of aurintricarboxylic acid as a potent hepatitis C virus replicase inhibitor Antiviral. Chem. Chemother. 20 2009 19 36
35. N. Kaushik-Basu, A. Bopda-Waffo, T.T. Talele, A. Basu, P.R. Costa, A.J. da Silva, S.G. Sarafianos, and F. Noel Identification and characterization of coumestans as novel HCV NS5B polymerase inhibitors Nucleic Acids Res. 36 2008 1482 1496
36. T.J. Ewing, S. Makino, A.G. Skillman, and I.D. Kuntz DOCK 4.0: search strategies for automated molecular docking of flexible molecule databases J. Comput. Aided Mol. Des. 15 2001 411 428
37. C.S. Ring, E. Sun, J.H. McKerrow, G.K. Lee, P.J. Rosenthal, I.D. Kuntz, and F.E. Cohen Structure-based inhibitor design by using protein models for the development of antiparasitic agents Proc. Natl. Acad. Sci. U. S. A 90 1993 3583 3587
38. B.K. Shoichet, R.M. Stroud, D.V. Santi, I.D. Kuntz, and K.M. Perry Structure-based discovery of inhibitors of thymidylate synthase Science 259 1993 1445 1450
39. C.C. Cheng, G.W. Shipps Jr., Z. Yang, N. Kawahata, C.A. Lesburg, J.S. Duca, J. Bandouveres, J.D. Bracken, C.K. Jiang, S. Agrawal, E. Ferrari, and H.C. Huang Inhibitors of hepatitis C virus polymerase: synthesis and characterization of novel 2-oxy-6-fluoro-N-((S)-1-hydroxy-3-phenylpropan-2-yl)- benzamides Bioorg. Med. Chem. Lett. 20 2010 2119 2124
40. S. Betzi, C. Eydoux, C. Bussetta, M. Blemont, P. Leyssen, C. Debarnot, M. Ben-Rahou, J. Haiech, M. Hibert, F. Gueritte, D.S. Grierson, J.L. Romette, J.C. Guillemot, J. Neyts, K. Alvarez, X. Morelli, H. Dutartre, and B. Canard Identification of allosteric inhibitors blocking the hepatitis C virus polymerase NS5B in the RNA synthesis initiation step Antiviral Res. 84 2009 48 59
41. V. Soriano, M.G. Peters, and S. Zeuzem New therapies for hepatitis C virus infection Clin. Infect. Dis. 48 2009 313 320
42. J.C. Lee, C.K. Tseng, K.J. Chen, K.J. Huang, C.K. Lin, and Y.T. Lin A cell-based reporter assay for inhibitor screening of hepatitis C virus RNA-dependent RNA polymerase Anal. Biochem. 403 2010 52 62
43. A.O. Prykhod'ko, O.Ya. Yakovenko, A.G. Golub, V.G. Bdzhola, and S.M. Yarmoluk Evaluation of 4H-4-chromenone derivatives as inhibitors of protein kinase CK2 Biopolym. Cell 21 2005 287 292
44. O. Yakovenko, A.A. Oliferenko, A.G. Golub, V.G. Bdzhola, and S.M. Yarmoluk The new method of distribution integrals evaluations for high throughput virtual screening Ukr. Bioorg. Acta 1 2007 52 62
45. O. Yakovenko, A.A. Oliferenko, V.G. Bdzhola, V.A. Palyulin, and N.S. Zefirov Kirchhoff atomic charges fitted to multipole moments: implementation for a virtual screening system J. Comput. Chem. 29 2008 1332 1343
46. E. Lindahl, and B. Hess D.v.d. Spoel, GROMACS 3.0: a package for molecular simulation and trajectory analysis J. Mol. Model. 7 2001 306 317
47. E. Ferrari, Z. He, R.E. Palermo, and H.C. Huang Hepatitis C virus NS5B polymerase exhibits distinct nucleotide requirements for initiation and elongation J. Biol. Chem. 283 2008 33893 33901