Insight into the structural features of pyrazolopyrimidine- and pyrazolopyridine-based B-RafV600E kinase inhibitors by computational explorations

Chemical Biology and Drug Design

Volumn 83, Issue 6, 2014, Pages 643-655

  Li, Yan ^a   Han, Chunxiao ^a   Wang, Jinghui ^a   Yang, Yinfeng ^a   Zhang, Jingxiao ^a   Zhang, Shuwei ^a   Yang, Ling ^b  

^a DALIAN UNIVERSITY OF TECHNOLOGY   (China)

^b DALIAN INSTITUTE OF CHEMICAL PHYSICS   (China)

Author keywords

3D QSAR; docking; md; Pyrazolopyrimidine and pyrazolopyridine based inhibitors

Indexed keywords

B RAF KINASE; B RAF KINASE INHIBITOR; PYRAZOLE DERIVATIVE; PYRAZOLOPYRIDINE DERIVATIVE; PYRAZOLOPYRIMIDINE DERIVATIVE; PYRIDINE DERIVATIVE; UNCLASSIFIED DRUG; PROTEIN KINASE INHIBITOR; PYRAZOLOPYRIDINE;

ARTICLE; COMPARATIVE MOLECULAR FIELD ANALYSIS; COMPARATIVE MOLECULAR SIMILARITY INDICES ANALYSIS; CRYSTAL STRUCTURE; DRUG CONFORMATION; DRUG RECEPTOR BINDING; ENZYME INHIBITION; HYDROGEN BOND; HYDROPHOBICITY; LIGAND BINDING; MOLECULAR DOCKING; MOLECULAR DYNAMICS; PRIORITY JOURNAL; PROTEIN MOTIF; QUANTITATIVE STRUCTURE ACTIVITY RELATION; BINDING SITE; CHEMICAL STRUCTURE; CHEMISTRY; DRUG EFFECTS; ENZYME ACTIVATION;

BINDING SITES; ENZYME ACTIVATION; MOLECULAR DYNAMICS SIMULATION; MOLECULAR STRUCTURE; PROTEIN KINASE INHIBITORS; PROTO-ONCOGENE PROTEINS B-RAF; PYRAZOLES; PYRIDINES; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 84901189082     PISSN: 17470277     EISSN: 17470285     Source Type: Journal    
DOI: 10.1111/cbdd.12276     Document Type: Article

References (66)

1. Leicht D.T., Balan V., Kaplun A., Gupta V.S., Kaplun L., Dobson M., Tzivion G., (2007) Raf kinases: function, regulation and role in human cancer. Biochim Biophys Acta; 1773: 1196-1212.
2. Bonner T., O'Brien S.J., Nash W.G., Rapp U.R., Morton C.C., Leder P., (1984) The human homologs of the raf (mil) oncogene are located on human chromosomes 3 and 4. Science; 223: 71-74.
3. Jansen H.W., Lurz R., Bister K., Bonner T.I., Mark G.E., Rapp U.R., (1984) Homologous cell-derived oncogenes in avian carcinoma virus MH2 and murine sarcoma virus 3611. Nature; 307: 281-284.
4. Moelling K., Heimann B., Beimling P., Rapp U.R., Sander T., (1984) Serine- and threonine-specific protein kinase activities of purified gag-mil and gag-raf proteins. Nature; 312: 558-561.
5. Peyssonnaux C., Eychène A., (2001) The Raf/MEK/ERK pathway: new concepts of activation. Biol Cell; 93: 53-62.
6. V600E. Part 1: the development of selective, orally bioavailable and efficacious inhibitors. ACS Med Chem Lett; 2: 342-347.
7. Malumbres M., Barbacid M., (2003) RAS oncogenes: the first 30 years. Nat Rev Cancer; 3: 459-465.
8. V600E ligand inhibition, selectivity and conformational stability: an in silico study. Mol Pharm; 6: 144-157.
9. Hagemann C., Rapp U.R., (1999) Isotype-specific functions of Raf kinases. Exp Cell Res; 253: 34-46.
10. Shih K.C., Lin C.Y., Zhou J., Chi H.C., Chen T.S., Wang C.C., Tseng H.W., Tang C.Y., (2011) Development of novel 3D-QSAR combination approach for screening and optimizing B-Raf inhibitors in silico. J Chem Inf Model; 51: 398-407.
11. Davies H., Bignell G.R., Cox C., Stephens P., Edkins S., Clegg S., Teague J., et al,. (2002) Mutations of the BRAF gene in human cancer. Nature; 417: 949-954.
12. Luo C., Xie P., Marmorstein R., (2008) Identification of BRAF inhibitors through in silico screening. J Med Chem; 51: 6121-6127.
13. Wan P.T.C., Garnett M.J., Roe S.M., Lee S., Duvaz D.N., Good V.M., Project C.G., Jones C.M., Marshall C.J., Springer C.J., Barford D., Marais R., (2004) Mechanism of activation of the RAF-ERK signaling pathway by oncogenic mutations of B-RAF. Cell; 116: 855-867.
14. Nourry A., Zambon A., Davies L., Duvaz I.N., Dijkstra H.P., Menard D., Gaulon C., Duvaz D.N., Suijkerbuijk B.M.J.M., Friedlos F., Manne H.A., Kirk R., Whittaker S., Marais R., Springer C.J., (2010) BRAF inhibitors based on an imidazo[4,5]pyridin-2-one scaffold and a meta substituted middle ring. J Med Chem; 53: 1964-1978.
15. Karasarides M., Chiloeches A., Hayward R., Duvaz D.N., Scanlon I., Friedlos F., Ogilvie L., Hedley D., Martin J., Marshall C.J., Springer C.J., Marais R., (2004) B-RAF is a therapeutic target in melanoma. Oncogene; 23: 6292-6298.
16. Roberts P.J., Der C.J., (2007) Targeting the Raf-MEK-ERK mitogen-activated protein kinase cascade for the treatment of cancer. Oncogene; 26: 3291-3310.
17. Yang Y., Qin J., Liu H., Yao X., (2011) Molecular dynamics simulation, free energy calculation and structure-based 3D-QSAR studies of B-RAF kinase inhibitors. J Chem Inf Model; 51: 680-692.
18. Liu Y., Gray N.S., (2006) Rational design of inhibitors that bind to inactive kinase conformations. Nat Chem Biol; 2: 358-364.
19. Pargellis C., Tong L., Churchill L., Cirillo P.F., Gilmore T., Graham A.G., Grob P.M., Hickey E.R., Moss N., Pav S., Regan J., (2002) Inhibition of p38 MAP kinase by utilizing a novel allosteric binding site. Nat Struct Biol; 9: 268-272.
20. Clara M., Jeff S., (2009) Targeting the RAF-MEK-ERK pathway in cancer therapy. Cancer Lett; 283: 125-134.
21. Kim D.H., Sim T., (2012) Novel small molecule Raf kinase inhibitors for targeted cancer therapeutics. Arch Pharm Res; 35: 605-615.
22. Ramnath N., Adjei A., (2007) Inhibitors of Raf kinase and MEK signaling. Update Cancer Ther; 2: 111-118.
23. Wilhelm S.M., Carter C., Tang L., Wilkie D., Mcnabola A., Rong H., Chen C., et al,. (2004) BAY 43-9006 exhibits broad spectrum oral antitumor activity and targets the RAF/MEK/ERK pathway and receptor tyrosine kinases involved in tumor progression and angiogenesis. Cancer Res; 64: 7099-7109.
24. V600E inhibitor, displays potent antitumor activity in preclinical melanoma models. Cancer Res; 70: 5518-5527.
25. Dhomen N., Marais R., (2009) BRAF signaling and targeted therapies in melanoma. Hematol Oncol Clin North Am; 23: 529-545.
26. Ott P.A., Hamilton A., Min C., Amiri S.S., Goldberg L., Yoon J., Yee H., Buckley M., Christos P.J., Wright J.J., Polsky D., Osman I., Liebes L., Pavlick A.C., (2010) A phase II trial of sorafenib in metastatic melanoma with tissue correlates. PLoS ONE; 5: e15588.
27. Wellbrock C., Hurlstone A., (2010) BRAF as therapeutic target in melanoma. Biochem Pharmacol; 80: 561-567.
28. V600E. Part 3: an increase in aqueous solubility via the disruption of crystal packing. Bioorg Med Chem Lett; 22: 912-915.
29. V600E kinase with favorable physicochemical and pharmacokinetic properties. Bioorg Med Chem Lett; 22: 1165-1168.
30. V600E. Part 2: structure-activity relationships. Bioorg Med Chem Lett; 21: 5533-5537.
31. Zhang S., (2011) Computer-aided drug discovery and development. Methods Mol Biol; 716: 23-38.
32. Liu J., Zhang H., Xiao Z., Wang F., Wang X., Wang Y., (2011) Combined 3D-QSAR, molecular docking and molecular dynamics study on derivatives of peptide epoxyketone and tyropeptin-boronic acid as inhibitors against the β5 subunit of human 20S proteasome. Int J Mol Sci; 12: 1807-1835.
33. Chung J.Y., Chung H.W., Cho S.J., Hah J.M., Cho A.E., (2010) QM/MM based 3D QSAR models for potent B-Raf inhibitors. J Comput Aided Mol Des; 24: 385-397.
34. Ai Y., Wang S.T., Tang C., Sun P.H., Song F.J., (2011) 3D-QSAR and docking studies on pyridopyrazinones as BRAF inhibitors. Med Chem Res; 20: 1298-1317.
35. Caballero J., Morales J.H.A., Jaque A.V., (2011) Investigation of the differences in activity between hydroxycycloalkyl N1 substituted pyrazole derivatives as inhibitors of B-Raf kinase by using docking, molecular dynamics, QM/MM, and fragment-based de novo design: study of binding mode of diastereomer compounds. J Chem Inf Model; 51: 2920-2931.
36. Liu J., Wang F., Ma Z., Wang X., Wang Y., (2011) Structural determination of three different series of compounds as Hsp90 inhibitors using 3D-QSAR modeling, molecular docking and molecular dynamics methods. Int J Mol Sci; 12: 946-970.
37. Cramer R.D., Bunce J.D., Patterson D.E., Frank I.E., (1988) Cross validation, bootstrapping, and partial least squares compared with multiple regression in conventional QSAR studies. Quant Struct Act Rel; 7: 18-25.
38. Klebe G., Abraham U., Mietzner T., (1994) Molecular similarity in a comparative analysis (CoMSIA) of drug molecules to correlate and predict their biological activity. J Med Chem; 37: 4130-4146.
39. Wei S., Ji Z., Zhang H., Zhang J., Wang Y., Wu W., (2011) Isolation, biological evaluation and 3D-QSAR studies of insecticidal/narcotic sesquiterpene polyol esters. J Mol Model; 17: 681-693.
40. Gasteiger J., Marsili M., (1980) Iterative partial equalization of orbital electronegativity-a rapid access to atomic charges. Tetrahedron; 36: 3219-3228.
41. Clark M., Cramer R.D., Opdenbosch N.V., (1989) Validation of the general purpose tripos 5.2 force field. J Comput Chem; 10: 982-1012.
42. Kothandan G., Gadhe C.G., Madhavan T., Choi C.H., Cho S.J., (2011) Docking and 3D-QSAR (quantitative structure activity relationship) studies of flavones, the potent inhibitors of p-glycoprotein targeting the nucleotide binding domain. Eur J Med Chem; 46: 4078-4088.
43. Li Y., Wang Y.H., Yang L., Zhang S.W., Liu C.H., Yang S.L., (2005) Comparison of steroid substrates and inhibitors of P-glycoprotein by 3D-QSAR analysis. J Mol Struct; 733: 111-118.
44. Zhang B., Li Y., Zhang H., Ai C., (2010) 3D-QSAR and molecular docking studies on derivatives of MK-0457, GSK1070916 and SNS-314 as inhibitors against aurora B kinase. Int J Mol Sci; 11: 4326-4347.
45. Jones G., Willett P., Glen R.C., Leach A.R., Taylor R., (1997) Development and validation of a genetic algorithm for flexible docking. J Mol Biol; 267: 727-748.
46. Verdonk M.L., Cole J.C., Hartshorn M.J., Murray C.W., Taylor R.D., (2003) Improved protein-ligand docking using GOLD. Proteins; 52: 609-623.
47. Berman H.M., Westbrook J., Feng Z., Gilliland G., Bhat T.N., Weissig H., Shindyalov I.N., Bourne P.E., (2000) The protein data bank. Nucleic Acids Res; 28: 235-242.
48. Case D.A., Darden T.A., Cheatham T.E. III, Simmerling C.L., Wang J., Duke R.E., Luo R., et al,. (2008) AMBER 10. San Francisco, CA, USA: University of California.
49. Wang J., Wolf R.M., Caldwell J.W., Kollman P.A., Case D.A., (2004) Development and testing of a general amber force field. J Comput Chem; 25: 1157-1174.
50. Jakalian A., Jack D.B., Bayly C.I., (2002) Fast, efficient generation of high-quality atomic charges. AM1-BCC model: II. Parameterization and validation. J Comput Chem; 23: 1623-1641.
51. Hornak V., Abel R., Okur A., Strockbine B., Roitberg A., Simmerling C., (2006) Comparison of multiple Amber force fields and development of improved protein backbone parameters. Proteins; 65: 712-725.
52. Wang J., Wang W., Kollman P.A., Case D.A., (2006) Antechamber, an accessory software package for molecular mechanics calculations. J Mol Graph Model; 25: 247-260.
53. Ryckaert J.P., Ciccotti G., Berendsen H.J.C., (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.
54. Essmann U., Perera L., Berkowitz M.L., Darden T., Lee H., Pedersen L.G., (1995) A smooth particle mesh Ewald method. J Comput Phys; 103: 8577-8594.
55. 2!. J Mol Graph Model; 20: 269-276.
56. Wu Q., Gao Q., Guo H., Li D., Wang J., Gao W., Han C., Li Y., Yang L., (2013) Inhibition mechanism exploration of quinoline derivatives as PDE10A inhibitors by in silico analysis. Mol BioSyst; 9: 386-397.
57. 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.
58. 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.
59. Chen J., Han X., Liu Q., Makriyannis A., Wang J., Xie X., (2006) 3D-QSAR studies of arylpyrazole antagonists of cannabinoid receptor subtypes CB1 and CB2. A combined NMR and CoMFA approach. J Med Chem; 49: 625-636.
60. da Cunha E.F.F., Sippl W., de Castro Ramalho T., Antunes O.A.C., de Alencastro R.B., Albuquerque M.G., (2009) 3D-QSAR CoMFA/CoMSIA models based on theoretical active conformers of HOE/BAY-793 analogs derived from HIV-1 protease inhibitor complexes. Eur J Med Chem; 44: 4344-4352.
61. Kitchen D.B., Decornez H., Furr J.R., Bajorath J., (2004) Docking and scoring in virtual screening for drug discovery: methods and applications. Nat Rev Drug Discov; 3: 935-949.
62. Bollag G., Tsai J., Zhang J., Zhang C., Ibrahim P., Nolop K., Hirth P., (2012) Vemurafenib: the first drug approved for BRAF-mutant cancer. Nat Rev Drug Discov; 11: 873-886.
63. Wood E.R., Truesdale A.T., McDonald O.B., Yuan D., Hassell A., Dickerson S.H., Ellis B., Pennisi C., Horne E., Lackey K., Alligood K.J., Rusnak D.W., Gilmer T.M., Shewchuk L., (2004) A unique structure for epidermal growth factor receptor bond to GW572016 (Lapatinib). Cancer Res; 64: 6652-6659.
64. Bollag G., Hirth P., Tsai J., Zhang J., Ibrahim P.N., Cho H., Spevak W., et al,. (2010) Clinical efficacy of a RAF inhibitor needs broad target blockade in BRAF-mutant melanoma. Nature; 467: 596-599.
65. Wang J., Li F., Li Y., Yang Y., Wang B., Zhang S., Yang L., (2013) Insight into the structural requirements of benzimidazole derivatives as interleukin-2 inducible t-cell kinase inhibitors by computational explorations. Int J Quantum Chem; 113: 2385-2396.
66. Karplus M., McCammon J.A., (2002) Molecular dynamics simulations of biomolecules. Nat Struct Mol Biol; 9: 646-652.