Docking and quantitative structure-activity relationship studies for 3-fluoro-4-(pyrrolo[2,1-f][1,2,4]triazin-4-yloxy)aniline, 3-fluoro-4-(1H- pyrrolo[2,3-b]pyridin-4-yloxy)aniline, and 4-(4-amino-2-fluorophenoxy)-2- pyridinylamine derivatives as c-Met kinase inhibitors

Journal of Computer-Aided Molecular Design

Volumn 25, Issue 4, 2011, Pages 349-369

  Caballero, Julio ^a   Quiliano, Miguel ^b   Alzate Morales, Jans H ^a   Zimic, Mirko ^b   Deharo, Eric ^c,d  

^a UNIVERSIDAD DE TALCA   (Chile)

^b UNIVERSIDAD PERUANA CAYETANO HEREDIA   (Peru)

^c UNIVERSITÉ DE TOULOUSE   (France)

^d INSTITUT DE RECHERCHE POUR LE DÉVELOPPEMENT   (Peru)

Author keywords

c Met kinase inhibitors; CoMSIA; Molecular docking; Quantitative structure activity relationships; Topological descriptors

Indexed keywords

ANILINE; COMPUTATIONAL CHEMISTRY; ENZYME INHIBITION; HYDROGEN BONDS; MOLECULAR GRAPHICS; STRUCTURES (BUILT OBJECTS); TOPOLOGY;

C-MEET KINASE INHIBITOR; COMPARATIVE MOLECULAR SIMILARITY ANALYSE; DESCRIPTORS; KINASE INHIBITORS; MOLECULAR DOCKING; MOLECULAR SIMILARITY; PREDICTIVE MODELS; QUANTITATIVE STRUCTURE ACTIVITY RELATIONSHIP; SIMILARITY ANALYSIS; TOPOLOGICAL DESCRIPTORS;

LINEAR REGRESSION;

3 FLUORO 4 (1H PYRROLO[2,3 B]PYRIDIN 4 YLOXY)ANILINE DERIVATIVE; 3 FLUORO 4 (PYRROLO[2,1 F][1,2,4]TRIAZIN 4 YLOXY)ANILINE DERIVATIVE; 4 (4 AMINO 2 FLUOROPHENOXY) 2 PYRIDINYLAMINE DERIVATIVE; PROTEIN KINASE INHIBITOR; SCATTER FACTOR RECEPTOR; UNCLASSIFIED DRUG;

ARTICLE; COMPARATIVE MOLECULAR SIMILARITY INDICES ANALYSIS; COMPLEX FORMATION; CONFORMATION; CONTROLLED STUDY; DATA ANALYSIS SOFTWARE; DRUG EFFECT; DRUG MECHANISM; DRUG PROTEIN BINDING; DRUG STRUCTURE; ENZYME ACTIVE SITE; ENZYME INHIBITION; HYDROGEN BOND; HYDROPHOBICITY; IC 50; MOLECULAR DOCKING; MULTIPLE LINEAR REGRESSION ANALYSIS; PREDICTION; PRIORITY JOURNAL; PROCESS DEVELOPMENT; QUANTITATIVE STRUCTURE ACTIVITY RELATION; STATIC ELECTRICITY; VALIDATION PROCESS;

EID: 79956188006     PISSN: 0920654X     EISSN: 15734951     Source Type: Journal    
DOI: 10.1007/s10822-011-9425-1     Document Type: Article

References (57)

1. X Liu W Yao RC Newton PA Scherle 2008 Targeting the c-MET signaling pathway for cancer therapy Expert Opin Investig Drugs 17 7 997 1011 10.1517/13543784.17.7.997 1:CAS:528:DC%2BD1cXntFymur8%3D
2. B Peruzzi DP Bottaro 2006 Targeting the c-Met signaling pathway in cancer Clin Cancer Res 12 12 3657 3660 10.1158/1078-0432.CCR-06-0818 1:CAS:528:DC%2BD28XlvVSls7c%3D (Pubitemid 44000247)
3. C-G Huh VM Factor A Sánchez K Uchida EA Conner SS Thorgeirsson 2004 Hepatocyte growth factor/c-met signaling pathway is required for efficient liver regeneration and repair Proc Natl Acad Sci USA 101 13 4477 4482 10.1073/pnas.0306068101 1:CAS:528:DC%2BD2cXjtFKju7c%3D (Pubitemid 38437436)
4. E Lesko M Majka 2008 The biological role of HGF-MET axis in tumor growth and development of metastasis Front Biosci 13 13 1271 1280 10.2741/2760 1:CAS:528:DC%2BD1cXhs1Cgsr0%3D (Pubitemid 351594710)
5. PM Comoglio S Giordano L Trusolino 2008 Drug development of MET inhibitors: targeting oncogene addiction and expedience Nat Rev Drug Discov 7 6 504 516 10.1038/nrd2530 1:CAS:528:DC%2BD1cXmsVOjsb0%3D (Pubitemid 351767118)
6. J Porter 2010 Small molecule c-Met kinase inhibitors: a review of recent patents Expert Opin Ther Pat 20 2 159 177 10.1517/13543770903514137 1:CAS:528:DC%2BC3cXhtVGktb8%3D
7. JP Eder GF Vande Woude SA Boerner PM LoRusso 2009 Novel therapeutic inhibitors of the c-Met signaling pathway in cancer Clin Cancer Res 15 7 2207 2214 10.1158/1078-0432.CCR-08-1306 1:CAS:528:DC%2BD1MXjvVWltrY%3D
8. GM Schroeder X-T Chen DK Williams DS Nirschl Z-W Cai D Wei JS Tokarski Y An J Sack, et al. 2008 Identification of pyrrolo[2, 1-f][1, 2, 4]triazine-based inhibitors of Met kinase Bioorg Med Chem Lett 18 6 1945 1951 10.1016/j.bmcl.2008.01.121 1:CAS:528:DC%2BD1cXjtlymsrY%3D (Pubitemid 351380893)
9. KS Kim L Zhang R Schmidt Z-W Cai D Wei DK Williams LJ Lombardo GL Trainor D Xie, et al. 2008 Discovery of pyrrolopyridine-pyridone based inhibitors of met kinase: synthesis, X-ray crystallographic analysis, and biological activities J Med Chem 51 17 5330 5341 10.1021/jm800476q 1:CAS:528: DC%2BD1cXps1KnsL8%3D
10. DK Williams X-T Chen C Tarby R Kaltenbach Z-W Cai JS Tokarski Y An JS Sack B Wautlet, et al. 2010 Design, synthesis and structure-activity relationships of novel biarylamine-based Met kinase inhibitors Bioorg Med Chem Lett 20 9 2998 3002 10.1016/j.bmcl.2010.01.042 1:CAS:528:DC%2BC3cXkvFCjtrw%3D
11. Z-W Cai D Wei GM Schroeder LAM Cornelius K Kim X-T Chen RJ Schmidt DK Williams JS Tokarski, et al. 2008 Discovery of orally active pyrrolopyridine- and aminopyridine-based Met kinase inhibitors Bioorg Med Chem Lett 18 11 3224 3229 10.1016/j.bmcl.2008.04.047 1:CAS:528:DC%2BD1cXms1yiu7s%3D (Pubitemid 351718330)
12. GM Schroeder Y An Z-W Cai X-T Chen C Clark LAM Cornelius J Dai J Gullo-Brown A Gupta, et al. 2009 Discovery of N-(4-(2-Amino-3-chloropyridin-4- yloxy)-3-fluorophenyl)-4-ethoxy-1-(4-fluorophenyl)-2-oxo-1, 2-dihydropyridine-3- carboxamide (BMS-777607), a selective and orally efficacious inhibitor of the met kinase superfamily J Med Chem 52 5 1251 1254 10.1021/jm801586s 1:CAS:528:DC%2BD1MXhvVCnsLc%3D
13. BK Albrecht J-C Harmange D Bauer L Berry C Bode AA Boezio A Chen D Choquette I Dussault, et al. 2008 Discovery and optimization of triazolopyridazines as potent and selective inhibitors of the c-Met Kinase† J Med Chem 51 10 2879 2882 10.1021/jm800043g 1:CAS:528: DC%2BD1cXkvFShtLk%3D (Pubitemid 351706015)
14. AA Boezio L Berry BK Albrecht D Bauer SF Bellon C Bode A Chen D Choquette I Dussault, et al. 2009 Discovery and optimization of potent and selective triazolopyridazine series of c-Met inhibitors Bioorg Med Chem Lett 19 22 6307 6312 10.1016/j.bmcl.2009.09.096 1:CAS:528:DC%2BD1MXhtlWlsrbF
15. ND D'Angelo SF Bellon SK Booker Y Cheng A Coxon C Dominguez I Fellows D Hoffman R Hungate, et al. 2008 Design, synthesis, and biological evaluation of potent c-Met inhibitors J Med Chem 51 18 5766 5779 10.1021/jm8006189
16. J Porter S Lumb F Lecomte J Reuberson A Foley M Calmiano K le Riche H Edwards J Delgado, et al. 2009 Discovery of a novel series of quinoxalines as inhibitors of c-Met kinase Bioorg Med Chem Lett 19 2 397 400 10.1016/j.bmcl.2008.11.062 1:CAS:528:DC%2BD1MXmtF2r
17. J Porter S Lumb RJ Franklin JM Gascon-Simorte M Calmiano KL Riche B Lallemand J Keyaerts H Edwards, et al. 2009 Discovery of 4-azaindoles as novel inhibitors of c-Met kinase Bioorg Med Chem Lett 19 10 2780 2784 10.1016/j.bmcl.2009.03.110 1:CAS:528:DC%2BD1MXltl2rsLY%3D
18. JH Alzate-Morales J Caballero A Vergara-Jaque FD González-Nilo 2009 Insights into the structural basis of N2 and O6 substituted guanine derivatives as cyclin-dependent kinase 2 (CDK2) inhibitors: prediction of the binding modes and potency of the inhibitors by docking and ONIOM calculations J Chem Inf Model 49 4 886 899 10.1021/ci8004034 1:CAS:528:DC%2BD1MXjvVegu7g%3D
19. JH Alzate-Morales A Vergara-Jaque J Caballero 2010 Computational study on the interaction of N1 substituted pyrazole derivatives with B-Raf kinase: an unusual water wire hydrogen-bond network and novel interactions at the entrance of the active site J Chem Inf Model 50 6 1101 1112 10.1021/ci100049h 1:CAS:528:DC%2BC3cXmvFKmu7o%3D
20. CA Larsen WH Bisson RH Dashwood 2009 Tea catechins inhibit hepatocyte growth factor receptor (MET Kinase) activity in human colon cancer cells: kinetic and molecular docking studies J Med Chem 52 21 6543 6545 10.1021/jm901330e 1:CAS:528:DC%2BD1MXht1Okur3N
21. M Fernandez A Tundidor-Camba J Caballero 2005 Modeling of cyclin-dependent kinase inhibition by 1H-Pyrazolo[3, 4-d]Pyrimidine derivatives using artificial neural network ensembles J Chem Inf Model 45 6 1884 1895 10.1021/ci050263i 1:CAS:528:DC%2BD2MXhtFSlu7fE (Pubitemid 41784762)
22. M González J Caballero A Helguera M Garriga G González M Fernández 2006 2D autocorrelation modelling of the inhibitory activity of cytokinin-derived cyclin-dependent kinase inhibitors Bull Math Biol 68 4 735 751 10.1007/s11538-005-9006-3 (Pubitemid 44195547)
23. J Caballero M Fernández M Saavedra FD González-Nilo 2008 2D Autocorrelation, CoMFA, and CoMSIA modeling of protein tyrosine kinases' inhibition by substituted pyrido[2, 3-d]pyrimidine derivatives Bioorg Med Chem 16 2 810 821 10.1016/j.bmc.2007.10.024 1:CAS:528:DC%2BD1cXhsFyqu70%3D (Pubitemid 351175639)
24. J Caballero M Fernández FD González-Nilo 2008 Structural requirements of pyrido[2, 3-d]pyrimidin-7-one as CDK4/D inhibitors: 2D autocorrelation, CoMFA and CoMSIA analyses Bioorg Med Chem 16 11 6103 6115 10.1016/j.bmc.2008.04.048 1:CAS:528:DC%2BD1cXmvFegtLg%3D (Pubitemid 351766716)
25. C Gueto JL Ruiz JE Torres J Méndez R Vivas-Reyes 2008 Three-dimensional quantitative structure-activity relationship studies on novel series of benzotriazine based compounds acting as Src inhibitors using CoMFA and CoMSIA Bioorg Med Chem 16 5 2439 2447 10.1016/j.bmc.2007.11.053 1:CAS:528:DC%2BD1cXjtl2murc%3D (Pubitemid 351380930)
26. J Alzate-Morales J Caballero 2010 Computational study of the interactions between guanine derivatives and cyclin-dependent kinase 2 (CDK2) by CoMFA and QM/MM J Chem Inf Model 50 1 110 122 10.1021/ci900302z 1:CAS:528: DC%2BD1MXhsF2qurnJ
27. D Muthas YA Sabnis M Lundborg A Karlén 2008 Is it possible to increase hit rates in structure-based virtual screening by pharmacophore filtering? An investigation of the advantages and pitfalls of post-filtering J Mol Graph Model 26 8 1237 1251 10.1016/j.jmgm.2007.11.005 1:CAS:528: DC%2BD1cXlvVWntr0%3D
28. H-Z Xie L-L Li J-X Ren J Zou L Yang Y-Q Wei S-Y Yang 2009 Pharmacophore modeling study based on known spleen tyrosine kinase inhibitors together with virtual screening for identifying novel inhibitors Bioorg Med Chem Lett 19 7 1944 1949 10.1016/j.bmcl.2009.02.049 1:CAS:528:DC%2BD1MXjt1arsrY%3D
29. M Uno HS Ban W Nabeyama H Nakamura 2008 de novo design and synthesis of N-benzylanilines as new candidates for VEGFR tyrosine kinase inhibitors Org Biomol Chem 6 6 979 981 10.1039/b719959g 1:CAS:528:DC%2BD1cXjtVCju7Y%3D
30. M Vieth J Erickson J Wang Y Webster M Mader R Higgs I Watson 2009 Kinase inhibitor data modeling and de novo inhibitor design with fragment approaches J Med Chem 52 20 6456 6466 10.1021/jm901147e 1:CAS:528:DC%2BD1MXhtF2ltLvM
31. JH Alzate-Morales R Contreras A Soriano I Tuñon E Silla 2007 A computational study of the protein-ligand interactions in CDK2 inhibitors: using quantum mechanics/molecular mechanics interaction energy as a predictor of the biological activity Biophys J 92 2 430 439 10.1529/biophysj.106.091512 1:CAS:528:DC%2BD2sXktVehtg%3D%3D (Pubitemid 46145776)
32. JH Alzate-Morales J Caballero FD Gonzalez-Nilo R Contreras 2009 A computational ONIOM model for the description of the H-bond interactions between NU2058 analogues and CDK2 active site Chem Phys Lett 479 1-3 149 155 10.1016/j.cplett.2009.08.020 1:CAS:528:DC%2BD1MXhtVKgsb7F
33. O Villacañas JJ Pérez J Rubio-Martínez 2002 Structural analysis of the inhibition of Cdk4 and Cdk6 by p16INK4a through molecular dynamics simulations J Biomol Struct Dyn 20 347 358 (Pubitemid 36019289)
34. Y Asses V Leroux S Tairi-Kellou R Dono F Maina B Maigret 2009 Analysis of c-Met kinase domain complexes: a new specific catalytic site receptor model for defining binding modes of ATP-competitive ligands Chem Biol Drug Des 74 6 560 570 10.1111/j.1747-0285.2009.00895.x 1:CAS:528:DC%2BD1MXhsVGku7bO
35. G Klebe U Abraham T Mietzner 1994 Molecular similarity indices in a comparative analysis (CoMSIA) of drug molecules to correlate and predict their biological activity J Med Chem 37 24 4130 4146 10.1021/jm00050a010 1:CAS:528:DyaK2cXmslWhu7Y%3D (Pubitemid 24379702)
36. B Wellenzohn KR Liedl BM Rode Zaheer-ul-haq 2003 Molecular docking studies of natural cholinesterase-inhibiting steroidal alkaloids from sarcococca saligna J Med Chem 46 23 5087 5090 10.1021/jm0309194 (Pubitemid 37352046)
37. LE Rojo J Alzate-Morales IN Saavedra P Davies RB Maccioni 2010 Selective interaction of lansoprazole and astemizole with tau polymers: potential new clinical use in diagnosis of alzheimer's disease J Alzheimer Dis 19 2 573 589 1:CAS:528:DC%2BC3cXht1Slt7s%3D
38. S Hanessian N Moitessier E Therrien 2001 A comparative docking study and the design of potentially selective MMP inhibitors J Comput Aided Mol Des 15 10 873 881 10.1023/A:1014356529909 1:CAS:528:DC%2BD38Xit1Gqs7s%3D (Pubitemid 34218291)
39. J Caballero A Vergara-Jaque M Fernández D Coll 2009 Docking and quantitative structure-activity relationship studies for sulfonyl hydrazides as inhibitors of cytosolic human branched-chain amino acid aminotransferase Mol Divers 13 4 493 500 10.1007/s11030-009-9140-1 1:CAS:528:DC%2BD1MXht1CmtrzF
40. CF Lagos J Caballero FD Gonzalez-Nilo C David Pessoa-Mahana T Perez-Acle 2008 Docking and quantitative structure-activity relationship studies for the bisphenylbenzimidazole family of non-nucleoside inhibitors of HIV-1 reverse transcriptase Chem Biol Drug Des 72 5 360 369 10.1111/j.1747-0285.2008.00716.x 1:CAS:528:DC%2BD1cXhtlOqtb%2FE
41. R Abagyan M Totrov D Kuznetsov 1994 ICM-A new method for protein modeling and design: Applications to docking and structure prediction from the distorted native conformation J Comput Chem 15 5 488 506 10.1002/jcc.540150503 1:CAS:528:DyaK2MXhtVWisA%3D%3D
42. Molecular Editor, version 2.5, La Jolla, CA, Molsoft LLC, 2006
43. ICM, version 3.4-8, La Jolla, CA, Molsoft LLC, 2006
44. J An M Totrov R Abagyan 2005 Pocketome via comprehensive identification and classification of ligand binding envelopes Mol Cell Proteomics 4 6 752 761 10.1074/mcp.M400159-MCP200 1:CAS:528:DC%2BD2MXlsV2nsro%3D (Pubitemid 40873004)
45. J Caballero M Fernández 2008 Artificial neural networks from MATLAB in medicinal chemistry. Bayesian-regularized genetic neural networks (BRGNN): application to the prediction of the antagonistic activity against human platelet thrombin receptor (PAR-1) Curr Top Med Chem 8 18 1580 1605 10.2174/156802608786786570 1:CAS:528:DC%2BD1MXhtlCgsbo%3D
46. DRAGON, version 3.0, Milano, Italy, Milano Chemometrics, 2003
47. V Consonni R Todeschini M Pavan 2002 Structure/response correlations and similarity/diversity analysis by GETAWAY descriptors. 1. Theory of the novel 3D molecular descriptors J Chem Inf Comput Sci 42 3 682 692 1:CAS:528: DC%2BD38XivFCgtrY%3D (Pubitemid 35355277)
48. M Fernández J Caballero 2007 QSAR modeling of matrix metalloproteinase inhibition by N-hydroxy-[alpha]-phenylsulfonylacetamide derivatives Bioorg Med Chem 15 18 6298 6310 10.1016/j.bmc.2007.06.014 (Pubitemid 47096793)
49. VN Viswanadhan AK Ghose GR Revankar RK Robins 1989 Atomic physicochemical parameters for three dimensional structure directed quantitative structure-activity relationships. 4. Additional parameters for hydrophobic and dispersive interactions and their application for an automated superposition of certain naturally occurring nucleoside antibiotics J Chem Inf Comput Sci 29 3 163 172 1:CAS:528:DyaL1MXkslSgs7w%3D
50. P Ertl B Rohde P Selzer 2000 Fast calculation of molecular polar surface area as a sum of fragment-based contributions and its application to the prediction of drug transport properties J Med Chem 43 20 3714 3717 10.1021/jm000942e 1:CAS:528:DC%2BD3cXmsFeitb4%3D
51. I Miroguchi S Hirono Q Liu I Nakagome Y Matsushita 1992 Simple method of calculating octanol/water partition coefficient Chem Pharm Bull 40 127 130
52. DB de Oliveira AC Gaudio 2000 BuildQSAR: a new computer program for QSAR analysis Quant Struct Act Relat 19 6 599 601 10.1002/1521-3838(200012)19: 6<599::AID-QSAR599>3.0.CO;2-B
53. MTD Cronin TW Schultz 2003 Pitfalls in QSAR J Mol Struct 622 1-2 39 51 1:CAS:528:DC%2BD3sXhsVSrurg%3D
54. M Fernandez MC Carreiras JL Marco J Caballero 2006 Modeling of acetylcholinesterase inhibition by tacrine analogues using Bayesian-regularized Genetic Neural Networks and ensemble averaging J Enzyme Inhib Med Chem 21 6 647 661 10.1080/14756360600862366 1:CAS:528:DC%2BD2sXnvFWluw%3D%3D (Pubitemid 44970953)
55. MH Fatemi S Gharaghani 2007 A novel QSAR model for prediction of apoptosis-inducing activity of 4-aryl-4-H-chromenes based on support vector machine Bioorg Med Chem 15 24 7746 7754 10.1016/j.bmc.2007.08.057 1:CAS:528:DC%2BD2sXhtF2msL3O (Pubitemid 47575917)
56. MP González C Terán M Teijeira MJ González-Moa 2005 GETAWAY descriptors to predicting A2A adenosine receptors agonists Eur J Med Chem 40 11 1080 1086 10.1016/j.ejmech.2005.04.014 (Pubitemid 41446277)
57. A Golbraikh A Tropsha 2002 Beware of q2! J Mol Graph Model 20 4 269 276 10.1016/S1093-3263(01)00123-1 1:CAS:528:DC%2BD3MXpt1art7o%3D (Pubitemid 34017544)