Exploring the crucial structural elements required for tricyclic quinoline analogs as protein kinase CK2 inhibitors by a combined computational analysis

Medicinal Chemistry Research

Volumn 22, Issue 9, 2013, Pages 4410-4422

  Zhou, Yue ^a   Zhang, Na ^a   Zhong, Rugang ^a  

^a BEIJING UNIVERSITY OF TECHNOLOGY   (China)

Author keywords

3D QSAR; CK2; CX 4945 analogs; Molecular docking; Molecular dynamics

Indexed keywords

CASEIN KINASE II; CASEIN KINASE II INHIBITOR; PROTEIN SERINE THREONINE KINASE INHIBITOR; QUINOLINE DERIVATIVE; UNCLASSIFIED DRUG;

ARTICLE; BINDING AFFINITY; COMPARATIVE MOLECULAR FIELD ANALYSIS; COMPARATIVE MOLECULAR SIMILARITY INDICES ANALYSIS; CONFORMATIONAL TRANSITION; HUMAN; HYDROGEN BOND; HYDROPHOBICITY; IC 50; ISOMER; MOLECULAR DOCKING; MOLECULAR DYNAMICS; QUANTITATIVE STRUCTURE ACTIVITY RELATION;

EID: 84881162547     PISSN: 10542523     EISSN: 15548120     Source Type: Journal    
DOI: 10.1007/s00044-012-0442-y     Document Type: Article

References (53)

1. Ahmad KA, Wang G, Unger G, Slaton J, Ahmed K (2008) Protein kinase CK2 - a key suppressor of apoptosis. Adv Enzyme Regul 48:179-187
2. Battistutta R (2009) Structural bases of protein kinase CK2 inhibition. Cell Mol Life Sci 66:1868-1889
3. Battistutta R, Mazzorana M, Sarno S, Kazimierczuk Z, Zanotti G, Pinna LA (2005) Inspecting the structure-activity relationship of protein kinase CK2 inhibitors derived from tetrabromo-benzimidazole. Chem Biol 12:1211-1219
4. Battistutta R, Mazzorana M, Cendron L, Bortolato A, Sarno S, Kazimierczuk Z, Zanotti G, Moro S, Pinna LA (2007) The ATP-binding site of protein kinase CK2 holds a positive electrostatic area and conserved water molecules. ChemBioChem 8:1804-1809
5. Battistutta R, Cozza G, Pierre F, Papinutto E, Lolli G, Sarno S, O'Brien SE, Siddiqui-Jain A, Haddach M, Anderes K, Ryckman DM, Meggio F, Pinna LA (2011) Unprecedented selectivity and structural determinants of a new class of protein kinase CK2 inhibitors in clinical trials for the treatment of cancer. Biochemistry 50:8478-8488
6. Berendsen HJC, Postma JPM, van Gunsteren WF, Di Nola A, Haak JR (1984) Molecular dynamics with coupling to an external bath. J Chem Phys 81:3684-3690
7. Böhm M, Stürzebecher J, Klebe G (1999) Three-dimensional quantitative structure-activity relationship analyses using comparative molecular field analysis and comparative molecular similarity indices analysis to elucidate selectivity differences of inhibitors binding to trypsin, thrombin, and factor Xa. J Med Chem 42:458-477
8. Bringmann G, Rummey C (2003) 3D QSAR investigations on antimalarial naphthylisoquinoline alkaloids by comparative molecular similarity indices analysis (CoMSIA), based on different alignment approaches. J Chem Inf Comput Sci 43:304-316
9. Cao DS, Liang YZ, Xu QS, Li HD, Chen X (2010) A new strategy of outlier detection for QSAR/QSPR. J Comput Chem 31:592-602
10. Case DA, Cheatham TE 3rd, Darden T, Gohlke H, Luo R, Merz KM Jr, Onufriev A, Simmerling C, Wang B, Woods RJ (2005) The Amber biomolecular simulation programs. J Comput Chem 26:1668-1688
11. Chilin A, Battistutta R, Bortolato A, Cozza G, Zanatta S, Poletto G, Mazzorana M, Zagotto G, Uriarte E, Guiotto A, Pinna LA, Meggio F, Moro S (2008) Coumarin as attractive casein kinase 2 (CK2) inhibitor scaffold: an integrate approach to elucidate the putative binding motif and explain structure-activity relationships. J Med Chem 51:752-759
12. Cozza G, Mazzorana M, Papinutto E, Bain J, Elliott M, di Maira G, Gianoncelli A, Pagano MA, Sarno S, Ruzzene M, Battistutta R, Meggio F, Moro S, Zagotto G, Pinna LA (2009) Quinalizarin as a potent, selective and cell-permeable inhibitor of protein kinase CK2. Biochem J 421:387-395
13. Cozza G, Bortolato A, Moro S (2010) How druggable is protein kinase CK2? Med Res Rev 30:419-462
14. Cozza G, Meggio F, Moro S (2011) The dark side of protein kinase CK2 inhibition. Curr Med Chem 18:2867-2884
15. Cramer RD, Patterson DE, Bunce JD (1988) Comparative molecular field analysis (CoMFA). 1. Effect of shape on binding of steroids to carrier proteins. J Am Chem Soc 110:5959-5967
16. (N) method for Ewald sums in large systems. J Chem Phys 98:10089-10094
17. Eddy SF, Guo S, Demicco EG, Romieu-Mourez R, Landesman-Bollag E, Seldin DC, Sonenshein GE (2005) Inducible IkappaB kinase/IkappaB kinase epsilon expression is induced by CK2 and promotes aberrant nuclear factor-kappaB activation in breast cancer cells. Cancer Res 65:11375-11383
18. Ferguson AD, Sheth PR, Basso AD, Paliwal S, Gray K, Fischmann TO, Le HV (2011) Structural basis of CX-4945 binding to human protein kinase CK2. FEBS Lett 585:104-110
19. Filhol O, Martiel JL, Cochet C (2004) Protein kinase CK2: a new view of an old molecular complex. EMBO Rep 5:351-355
20. Fox T, Kollman PA (1998) Application of the RESP methodology in the parametrization of organic solvents. J Phys Chem B 102:8070-8079
21. Gasteiger J, Marsili M (1980) Iterative partial equalization of orbital electro negativity - a rapid access to atomic charges. Tetrahedron 36:3219-3228
22. Guerra B, Issinger OG (2008) Protein kinase CK2 in human diseases. Curr Med Chem 15:1870-1886
23. Haddach M, Pierre F, Regan CF, Borsan C, Michaux J, Stefan E, Kerdoncuff P, Schwaebe MK, Chua PC, Siddiqui-Jain A, Macalino D, Drygin D, O'Brien SE, Rice WG, Ryckman DM (2012) Synthesis and SAR of inhibitors of protein kinase CK2: novel tricyclic quinoline analogs. Bioorg Med Chem Lett 22:45-48
24. Hou Z, Nakanishi I, Kinoshita T, Takei Y, Yasue M, Misu R, Suzuki Y, Nakamura S, Kure T, Ohno H, Murata K, Kitaura K, Hirasawa A, Tsujimoto G, Oishi S, Fujii N (2012) Structure-based design of novel potent protein kinase CK2 (CK2) inhibitors with phenyl-azole scaffolds. J Med Chem 55:2899-2903
25. Huang HJ, Yu HW, Chen CY, Hsu CH, Chen HY, Lee KJ, Tsai FJ, Chen CYC (2010) Current developments of computer-aided drug design. J Taiwan Inst Chem Eng 41:623-635
26. Jones G, Willett P, Glen RC, Leach AR, Taylor R (1997) Development and validation of a genetic algorithm for flexible docking. J Mol Biol 267:727-748
27. Jorgensen WL, Chandrasekhar J, Madura JD, Impey RW, Klein ML (1983) Comparison of simple potential functions for simulating liquid water. J Chem Phys 79:926-935
28. Klebe G, Abraham U, Mietzner T (1994) Molecular similarity indices in a comparative analysis (CoMSIA) of drug molecules to correlate and predict their biological activity. J Med Chem 37:4130-4146
29. Li Y, Luan Y, Qi X, Li M, Gong L, Xue X, Wu X, Wu Y, Chen M, Xing G, Yao J, Ren J (2010) Emodin triggers DNA double-strand breaks by stabilizing topoisomerase II-DNA cleavage complexes and by inhibiting ATP hydrolysis of topoisomerase II. Toxicol Sci 118:435-443
30. Litchfield DW (2003) Protein kinase CK2: structure, regulation and role in cellular decisions of life and death. Biochem J 369:1-15
31. Liu H, Wang X, Wang J, Wang J, Li Y, Yang L, Li G (2011) Structural determinants of CX-4945 derivatives as protein kinase CK2 inhibitors: a computational study. Int J Mol Sci 12:7004-7021
32. Mazzorana M, Pinna LA, Battistutta R (2008) A structural insight into CK2 inhibition. Mol Cell Biochem 316:57-62
33. Meggio F, Pinna LA (2003) One-thousand-and-one substrates of protein kinase CK2? Faseb J 17:349-368
34. Morshed MN, Muddassar M, Pasha FA, Cho SJ (2009) Pharmacophore identification and validation study of CK2 inhibitors using CoMFA/CoMSIA. Chem Biol Drug Des 74:148-158
35. Niefind K, Guerra B, Ermakowa I, Issinger OG (2001) Crystal structure of human protein kinase CK2: insights into basic properties of the CK2 holoenzyme. EMBO J 20:5320-5331
36. Pagano MA, Bain J, Kazimierczuk Z, Sarno S, Ruzzene M, Di Maira G, Elliott M, Orzeszko A, Cozza G, Meggio F, Pinna LA (2008) The selectivity of inhibitors of protein kinase CK2: an update. Biochem J 415:353-365
37. Papinutto E, Ranchio A, Lolli G, Pinna LA, Battistutta R (2012) Structural and functional analysis of the flexible regions of the catalytic α-subunit of protein kinase CK2. J Struct Biol 177:382-391
38. Perez DI, Gil C, Martinez A (2011) Protein kinases CK1 and CK2 as new targets for neurodegenerative diseases. Med Res Rev 31:924-954
39. Pierre F, Chua PC, O'Brien SE, Siddiqui-Jain A, Bourbon P, Haddach M, Michaux J, Nagasawa J, Schwaebe MK, Stefan E, Vialettes A, Whitten JP, Chen TK, Darjania L, Stansfield R, Anderes K, Bliesath J, Drygin D, Ho C, Omori M, Proffitt C, Streiner N, Trent K, Rice WG, Ryckman DM (2011a) Discovery and SAR of 5-(3-chlorophenylamino)benzo[c][2,6]naphthyridine-8-carboxylic acid (CX-4945), the first clinical stage inhibitor of protein kinase CK2 for the treatment of cancer. J Med Chem 54:635-654
40. Pierre F, O'Brien SE, Haddach M, Bourbon P, Schwaebe MK, Stefan E, Darjania L, Stansfield R, Ho C, Siddiqui-Jain A, Streiner N, Rice WG, Anderes K, Ryckman DM (2011b) Novel potent pyrimido[4,5-c]quinoline inhibitors of protein kinase CK2: SAR and preliminary assessment of their analgesic and anti-viral properties. Med Chem Lett 21:1687-1691
41. Poole A, Poore T, Bandhakavi S, McCann RO, Hanna DE, Glover CV (2005) A global view of CK2 function and regulation. Mol Cell Biochem 274:163-170
42. Ruzzene M, Pinna LA (2010) Addiction to protein kinase CK2: a common denominator of diverse cancer cells? Biochim Biophys Acta 1804:499-504
43. Ryckaert JP, Ciccotti G, Berendsen HJC (1977) Numerical integration of the cartesian equations of motion of a system with constraints:molecular dynamics of n-alkanes. J Comput Phys 23:327-341
44. Sarno S, de Moliner E, Ruzzene M, Pagano MA, Battistutta R, Bain J, Fabbro D, Schoepfer J, Elliott M, Furet P, Meggio F, Zanotti G, Pinna LA (2003) Biochemical and three-dimensional-structural study of the specific inhibition of protein kinase CK2 by [5-oxo-5,6-dihydroindolo-(1,2-a)quinazolin-7-yl]acetic acid (IQA). Biochem J 374:639-646
45. Sarno S, Papinutto E, Franchin C, Bain J, Elliott M, Meggio F, Kazimierczuk Z, Orzeszko A, Zanotti G, Battistutta R, Pinna LA (2011) ATP site-directed inhibitors of protein kinase CK2: an update. Curr Top Med Chem 11:1340-1351
46. Scaglioni PP, Yung TM, Cai LF, Erdjument-Bromage H, Kaufman AJ, Singh B, Teruya-Feldstein J, Tempst P, Pandolfi PP (2006) A CK2-dependent mechanism for degradation of the PML tumor suppressor. Cell 126:269-283
47. Sean E (2011) Oral small molecule inhibitor of CK2 protein kinase enables diverse drug combinations with improved treatment outcomes for cancer. Cylene Pharmaceuticals. http://www.cylenepharma.com/sites/default/files/files/Cylene- CK2-Program-%20Summary.pdf. Accessed 22 Mar 2011
48. Sekiguchi Y, Nakaniwa T, Kinoshita T, Nakanishi I, Kitaura K, Hirasawa A, Tsujimoto G, Tada T (2009) Structural insight into human CK2 alpha in complex with the potent inhibitor ellagic acid. Bioorg Med Chem Lett 19:2920-2923
49. Singh NN, Ramji DP (2008) Protein kinase CK2, an important regulator of the inflammatory response? J Mol Med 86:887-897
50. Ståhle L, Wold S (1987) Partial least squares analysis with cross-validation for the two-class problem: a Monte Carlo study. J Chemom 1:185-196
51. Thaimattam R, Daga PR, Banerjee R, Iqbal J (2005) 3D-QSAR studies on c-Src kinase inhibitors and docking analyses of a potent dual kinase inhibitor of c-Src and c-Abl kinases. Bioorg Med Chem 13:4704-4712
52. Tripos (2008) Sybyl 8.1. Tripos Inc, St. Louis, MO
53. Zhang N, Zhong R (2010) Docking and 3D-QSAR studies of 7-hydroxycoumarin derivatives as CK2 inhibitors. Eur J Med Chem 45:292-297