Pharmacophore modeling and virtual screening studies to identify new c-Met inhibitors

Journal of Molecular Modeling

Volumn 18, Issue 7, 2012, Pages 3087-3100

  Tai, Wenting ^a   Lu, Tao ^a   Yuan, Haoliang ^a   Wang, Fengxiao ^a   Liu, Haichun ^a   Lu, Shuai ^a   Leng, Ying ^a   Zhang, Weiwei ^a   Jiang, Yulei ^a   Chen, Yadong ^a  

^a CHINA PHARMACEUTICAL UNIVERSITY   (China)

Author keywords

C Met inhibitors; Cancer; Molecular docking; Pharmacophore modeling; Virtual screening

Indexed keywords

AMG 208; CRIZOTINIB; JNJ 38877605; MK 2461; PF 04217903; PROTEIN INHIBITOR; UNCLASSIFIED DRUG;

ARTICLE; DRUG IDENTIFICATION; DRUG SCREENING; IC 50; MOLECULAR DOCKING; MOLECULAR MODEL; PHARMACOPHORE; PRIORITY JOURNAL; RANDOMIZATION; RECEIVER OPERATING CHARACTERISTIC;

COMPUTER SIMULATION; DATABASES, FACTUAL; HYDROGEN BONDING; HYDROPHOBIC AND HYDROPHILIC INTERACTIONS; MODELS, MOLECULAR; PROTEIN BINDING; PROTEIN KINASE INHIBITORS; PROTO-ONCOGENE PROTEINS C-MET; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP; REPRODUCIBILITY OF RESULTS; ROC CURVE;

EID: 84864712912     PISSN: 16102940     EISSN: 09485023     Source Type: Journal    
DOI: 10.1007/s00894-011-1328-5     Document Type: Article

References (34)

1. Dancey J, Sausville EA (2003) Issues and progress with protein kinase inhibitors for cancer treatment. Nat Rev Drug Discov 2:296-313
2. Baselga J (2006) Targeting tyrosine kinases in cancer: the second wave. Science 312:1175-1178
3. Christensen JG, Burrows J, Salgia R (2005) c-Met as a target for human cancer and characterization of inhibitors for therapeutic intervention. Cancer Lett 225:1-26
4. Qian CN, Guo X, Cao B, Kort EJ, Lee CC, Chen J, Wang LM, Mai WY, Min HQ, Hong MH, Vande Woude GF, Resau JH, Teh BT (2002) Met protein expression level correlates with survival in patients with late-stage nasopharyngeal carcinoma. Cancer Res 62:589-596
5. Canadas I, Rojo F, Arumi-Uria M, Rovira A, Albanell J, Arriola E (2010) C-MET as a new therapeutic target for the development of novel anticancer drugs. Clin Transl Oncol 12:253-260
6. Underiner TL, Herbertz T, Miknyoczki SJ (2010) Discovery of small molecule c-Met inhibitors: Evolution and profiles of clinical candidates. Anticancer Agents Med Chem 10:7-27
7. Dussault I, Bellon SF (2009) From concept to reality: the long road to c-Met and RON receptor tyrosine kinase inhibitors for the treatment of cancer. Anticancer Agents Med Chem 9:221-229
8. Porter J (2010) Small molecule c-Met kinase inhibitors: a review of recent patents. Expert Opin Ther Pat 20:159-177
9. Liu X, Newton RC, Scherle PA (2009) Developing c-MET pathway inhibitors for cancer therapy: progress and challenges. Trends Mol Med 16:37-45
10. Liang Z, Zhang D, Ai J, Chen L, Wang H, Kong X, Zheng M, Liu H, Luo C, Geng M, Jiang H, Chen K (2011) Identification and synthesis of N' (2-oxoindolin-3-ylidene) hydrazide derivatives against c-Met kinase. Bioorg Med Chem Lett 21:3749-3754
11. Yuan H, Lu T, Ran T, Liu H, Lu S, Tai W, Leng Y, Zhang W, Wang J, Chen Y (2011) Novel strategy for three-dimensional fragmentbased lead discovery. J Chem Inf Model 51:959-974
12. Sakkiah S, Thangapandian S, John S, Kwon YJ, Lee KW (2010) 3D QSAR pharmacophore based virtual screening and molecular docking for identification of potential HSP90 inhibitors. Eur J Med Chem 45:2132-2140
13. Boezio AA, Berry L, Albrecht BK, Bauer D, Bellon SF, Bode C, Chen A, Choquette D, Dussault I, Fang M, Hirai S, Kaplan-Lefko P, Larrow JF, Lin MH, Lohman J, Potashman MH, Qu Y, Rex K, Santostefano M, Shah K, Shimanovich R, Springer SK, Teffera Y, Yang Y, Zhang Y, Harmange JC (2009) Discovery and optimization of potent and selective triazolopyridazine series of c-Met inhibitors. Bioorg Med Chem Lett 19:6307-6312
14. Albrecht BK, Harmange JC, Bauer D, Berry L, Bode C, Boezio AA, Chen A, Choquette D, Dussault I, Fridrich C, Hirai S, Hoffman D, Larrow JF, Kaplan-Lefko P, Lin J, Lohman J, Long AM, Moriguchi J, O'fConnor A, Potashman MH, Reese M, Rex K, Siegmund A, Shah K, Shimanovich R, Springer SK, Teffera Y, Yang Y, Zhang Y, Bellon SF (2008) Discovery and optimization of triazolopyridazines as potent and selective inhibitors of the c-Met kinase. J Med Chem 51:2879-2882
15. Porter J, Lumb S, Franklin RJ, Gascon-Simorte JM, Calmiano M, Riche KL, Lallemand B, Keyaerts J, Edwards H, Maloney A, Delgado J, King L, Foley A, Lecomte F, Reuberson J, Meier C, Batchelor M (2009) Discovery of 4-azaindoles as novel inhibitors of c-Met kinase. Bioorg Med Chem Lett 19:2780-2784
16. Nishii H, Chiba T, Morikami K, Fukami TA, Sakamoto H, Ko K, Koyano H (2010) Discovery of 6-benzyloxyquinolines as c-Met selective kinase inhibitors. Bioorg Med Chem Lett 20:1405-14099
17. Porter J, Lumb S, Lecomte F, Reuberson J, Foley A, Calmiano M, le Riche K, Edwards H, Delgado J, Franklin RJ, Gascon-Simorte JM, Maloney A, Meier C, Batchelor M (2009) Discovery of a novel series of quinoxalines as inhibitors of c-Met kinase. Bioorg Med Chem Lett 19:397-400
18. Koolman H, Heinrich T, Bottcher H, Rautenberg W, Reggelin M (2009) Syntheses of novel 2, 3-diaryl-substituted 5-cyano-4-azaindoles exhibiting c-Met inhibition activity. Bioorg Med Chem Lett 19:1879-1882
19. Cho SY, Han SY, Ha JD, Ryu JW, Lee CO, Jung H, Kang NS, Kim HR, Koh JS, Lee J (2010) Discovery of aminopyridines substituted with benzoxazole as orally active c-Met kinase inhibitors. Bioorg Med Chem Lett 20:4223-4227
20. Thangapandian S, John S, Sakkiah S, Lee KW (2011) Pharmacophore-based virtual screening and Bayesian model for the identification of potential human leukotriene A4 hydrolase inhibitors. Eur JMed Chem 46:1593-1603
21. John S, Thangapandian S, Sakkiah S, Lee KW (2010) Identification of potent virtual leads to design novel indoleamine 2, 3-dioxygenase inhibitors: pharmacophore modeling and molecular docking studies. Eur J Med Chem 45:4004-4012
22. Debnath AK (2002) Pharmacophore mapping of a series of 2, 4-diamino-5-deazapteridine inhibitors of Mycobacterium avium complex dihydrofolate reductase. J Med Chem 45:41-53
23. Li HF, Lu T, Zhu T, Jiang YJ, Rao SS, Hu LY, Xin BT, Chen YD (2009) Virtual screening for Raf-1 kinase inhibitors based on pharmacophore model of substituted ureas. Eur J Med Chem 44:1240-1249
24. Thangapandian S, John S, Sakkiah S, Lee KW (2010) Dockingenabled pharmacophore model for histone deacetylase 8 inhibitors and its application in anti-cancer drug discovery. J Mol Graph Model 29:382-395
25. Macdougall IJ, Griffith R (2008) Pharmacophore design and database searching for selective monoamine neurotransmitter transporter ligands. J Mol Graph Model 26:1113-1124
26. Bharatham N, Bharatham K, Lee KW (2007) Pharmacophore identification and virtual screening for methionyl-tRNA synthetase inhibitors. J Mol Graph Model 25:813-823
27. Fang C, Xiao Z, Guo Z (2011) Generation and validation of the first predictive pharmacophore model for cyclin-dependent kinase 9 inhibitors. J Mol Graph Model 29:800-808
28. Chen XM, Lu T, Lu S, Li HF, Yuan HL, Ran T, Liu HC, Chen YD (2010) Structure-based and shape-complemented pharmacophore modeling for the discovery of novel checkpoint kinase 1 inhibitors. J Mol Model 16:1195-1204
29. Triballeau N, Acher F, Brabet I, Pin JP, Bertrand HO (2005) Virtual screening workflow development guided by the "receiver operating characteristic" curve approach. Application to high-throughput docking on metabotropic glutamate receptor subtype 4. J Med Chem 48:2534-2547
30. Zou J, Xie HZ, Yang SY, Chen JJ, Ren JX, Wei YQ (2008) Towards more accurate pharmacophore modeling: multicomplex-based comprehensive pharmacophore map and most-frequent-feature pharmacophore model of CDK2. J Mol Graph Model 27:430-438
31. Thangapandian S, John S, Sakkiah S, Lee KW (2011) Potential virtual lead identification in the discovery of renin inhibitors: application of ligand and structure-based pharmacophore modeling approaches. Eur J Med Chem 46:2469-2476
32. Vangrevelinghe E, Zimmermann K, Schoepfer J, Portmann R, Fabbro D, Furet P (2003) Discovery of a potent and selective protein kinase CK2 inhibitor by high-throughput docking. J Med Chem 46:2656-2662
33. Tikhonova IG, Sum CS, Neumann S, Engel S, Raaka BM, Costanzi S, Gershengorn MC (2008) Discovery of novel agonists and antagonists of the free fatty acid receptor 1 (FFAR1) using virtual screening. J Med Chem 51:625-633
34. Rollinger JM, Steindl TM, Schuster D, Kirchmair J, Anrain K, Ellmerer EP, Langer T, Stuppner H, Wutzler P, Schmidtke M (2008) Structure-based virtual screening for the discovery of natural inhibitors for human rhinovirus coat protein. J Med Chem 51:842-851