Identification of novel inhibitors for Pim-1 kinase using pharmacophore modeling based on a novel method for selecting pharmacophore generation subsets

Journal of Computer-Aided Molecular Design

Volumn 30, Issue 1, 2016, Pages 39-68

  Shahin, Rand ^a   Swellmeen, Lubna ^a   Shaheen, Omar ^b   Aboalhaija, Nour ^a   Habash, Maha ^c  

^a ZARQA UNIVERSITY   (Jordan)

^b THE UNIVERSITY OF JORDAN   (Jordan)

^c APPLIED SCIENCE PRIVATE UNIVERSITY   (Jordan)

Author keywords

Discovery studio; Ligand base; Pharmacophore modelling; Pim 1 kinase; QSAR

Indexed keywords

BINDING ENERGY; COMPUTATIONAL CHEMISTRY; DISEASES; GENETIC ALGORITHMS; MOLECULAR GRAPHICS; MULTIPLE LINEAR REGRESSION; STUDIOS; VIRUSES;

BINDING POCKETS; DISCOVERY STUDIO; KINASE INHIBITORS; LIGAND BASE; MODEL-BASED OPC; PHARMACOPHORE MODELS; PHARMACOPHORES; PIM 1 KINASE; QUANTITATIVE STRUCTURE ACTIVITY RELATIONSHIP; RELATIONSHIP EQUATIONS;

LIGANDS;

ACRIDINE DERIVATIVE; ALANINE DERIVATIVE; ASPARAGINE DERIVATIVE; ASPARTIC ACID DERIVATIVE; BENZENE DERIVATIVE; CARBOXYLIC ACID; GLUTAMIC ACID; HYDROXYL GROUP; LEUCINE; LYSINE DERIVATIVE; METHYL GROUP; NITROGEN DERIVATIVE; PIM 1 KINASE INHIBITOR; PROTEIN KINASE PIM 1; PROTEIN SERINE THREONINE KINASE INHIBITOR; UNCLASSIFIED DRUG; VALINE; LIGAND; PROTEIN BINDING; PROTEIN KINASE INHIBITOR;

AREA UNDER THE CURVE; ARTICLE; BINDING SITE; BIOLOGICAL ACTIVITY; CHEMICAL INTERACTION; CHEMICAL STRUCTURE; COMPUTER MODEL; CONCENTRATION (PARAMETERS); CONTROLLED STUDY; COST; DRUG ACTIVITY; DRUG POTENCY; DRUG SCREENING; ELECTRON TRANSPORT; ENZYME BINDING; ENZYME INHIBITION; GENETIC ALGORITHM; HINGE REGION; HYDROGEN BOND; HYDROPHOBICITY; IC50; IN VITRO STUDY; IONIZATION; MOLECULAR DOCKING; MOLECULAR MODEL; MOLECULAR WEIGHT; MOUSE; NONHUMAN; NULL HYPOTHESIS; PHARMACOPHORE; PRIORITY JOURNAL; PROTEIN PROTEIN INTERACTION; QUANTITATIVE STRUCTURE ACTIVITY RELATION; RECEIVER OPERATING CHARACTERISTIC; STATIC ELECTRICITY; ANTAGONISTS AND INHIBITORS; CHEMISTRY; DRUG DEVELOPMENT; HUMAN; METABOLISM;

BINDING SITES; DRUG DISCOVERY; HUMANS; LIGANDS; MOLECULAR DOCKING SIMULATION; PROTEIN BINDING; PROTEIN KINASE INHIBITORS; PROTO-ONCOGENE PROTEINS C-PIM-1; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 84953354524     PISSN: 0920654X     EISSN: 15734951     Source Type: Journal    
DOI: 10.1007/s10822-015-9887-7     Document Type: Article

References (56)

1. Nawijn MC, Alendar A, Berns A (2011) For better or for worse: the role of Pim oncogenes in tumorigenesis. Nat Rev Cancer 11(1):23-34
2. Bachmann M, Kosan C, Xing PX, Montenarh M, Hoffmann I, Möröy T (2006) The oncogenic serine/threonine kinase Pim-1 directly phosphorylates and activates the G2/M specific phosphatase Cdc25C. Int J Biochem Cell Biol 38(3):430-443
3. Sliman F, Blairvacq M, Durieu E, Meijer L, Rodrigo J, Desmaele D (2010) Identification and structure-activity relationship of 8-hydroxy-quinoline-7-carboxylic acid derivatives as inhibitors of Pim-1 kinase. Bioorg Med Chem Lett 20(9):2801-2805
4. Bullock AN, Debreczeni JE, Fedorov OY, Nelson A, Marsden BD, Knapp S (2005) Structural basis of inhibitor specificity of the human protooncogene proviral insertion site in moloney murine leukemia virus (PIM-1) kinase. J Med Chem 48(24):7604-7614
5. Xiang Y, Hirth B, Asmussen G, Biemann H-P, Bishop KA, Good A, Fitzgerald M, Gladysheva T, Jain A, Jancsics K, Liu J, Metz M, Papoulis A, Skerlj R, Stepp JD, Wei RR (2011) The discovery of novel benzofuran-2-carboxylic acids as potent Pim-1 inhibitors. Bioorg Med Chem Lett 21(10):3050-3056
6. Warfel NA, Kraft AS (2015) PIM kinase (and Akt) biology and signaling in tumors. Parmacol Therapeutic 151:41-49
7. Suchaud V, Gavara L, Saugues E, Nauton L, Thery V, Anizon F, Moreau P (2013) Identification of 1,6-dihydropyrazolo[4,3-c]carbazoles and 3,6-dihydropyrazolo[3,4-c]carbazoles as new Pim kinase inhibitors. Bioorg Med Chem 21:4102-4111
8. Eichmann A, Yuan L, Bréant C, Alitalo K, Koskinen PJ (2000) Developmental expression of pim kinases suggests functions also outside of the hematopoietic system. Oncogene 19(9):1215-1224
9. Backes A, Zech B, Felber B, Klebl B, Müller G (2008) Small-molecule inhibitors binding to protein kinases. Part I exceptions from the traditional pharmacophore approach of type I inhibition. Expert Opin Drug Discov 3(12):1409-1425
10. Akue-Gedu R, Nauton L, Thery V, Bain J, Cohen P, Anizon F, Moreau P (2010) Synthesis Pim kinase inhibitory potencies and in vitro antiproliferative activities of diversely substituted pyrrolo[2,3-a]carbazoles. Bioorg Med Chem 18(18):6865-6873
11. Akue-Gedu R, Rossignol E, Azzaro S, Knapp S, Filippakopoulos P, Bullock AN, Bain J, Cohen P, Prudhomme M, Anizon F, Moreau P (2009) Synthesis kinase inhibitory potencies and in vitro antiproliferative evaluation of new Pim kinase inhibitors. J Med Chem 52(20):6369-6381
12. Cheney IW, Yan S, Appleby T, Walker H, Vo T, Yao N, Hamatake R, Hong Z, Wu JZ (2007) Identification and structure-activity relationships of substituted pyridones as inhibitors of Pim-1 kinase. Bioorg Med Chem Lett 17(6):1679-1683
13. Nishiguchi GA, Atallah G, Bellamacina C, Burger MT, Ding Y, Feucht PH, Garcia PD, Han W, Klivansky L, Lindvall M (2011) Discovery of novel 3,5-disubstituted indole derivatives as potent inhibitors of Pim-1, Pim-2, and Pim-3 protein kinases. Bioorg Med Chem Lett 21:6366-6369
14. Pastor J, Oyarzabal J, Saluste G, Alvarez RM, Rivero V, Ramos F, Cendon E, Blanco-Aparicio C, Ajenjo N, Cebria A, Albarran MI, Cebrian D, Corrionero A, Fominaya J, Montoya G, Mazzorana M (2012) Hit to lead evaluation of 1,2,3-triazolo[4,5-b]pyridines as PIM kinase inhibitors. Bioorg Med Chem Lett 22:1591-1597
15. Pierce AC, Jacobs M, Stuver-Moody C (2008) Docking study yields four novel inhibitors of the protooncogene Pim-1 kinase. J Med Chem 51:1972-1975
16. Pierre F, Stefan E, Nedellec AS, Chevrel MC, Regan CF, Siddiqui-Jain A, Macalino D, Streiner N, Drygin D, Haddach M, O'Brien SE, Anderes K, Ryckman DM (2011) 7-(4H-1,2,4-Triazol-3-yl)benzo[c][2,6]naphthyridines a novel class of Pim kinase inhibitors with potent cell antiproliferative activity. Bioorg Med Chem Lett 21:6687-6692
17. Ren JX, Li LL, Zheng RL, Xie HZ, Cao ZX, Feng S, Pan YL, Chen X, Wei YQ, Yang SYJ (2011) Discovery of novel Pim-1 kinase inhibitors by a hierarchical multistage virtual screening approach based on SVM model, pharmacophore, and molecular docking. Chem Inf Model 51:1364-1375
18. Tsuhako AL, Brown DS, Koltun ES, Aay N, Arcalas A, Chan V, Du H, Engst S, Franzini M, Galan A, Huang P, Johnston S, Kane B, Kim MH, Laird AD, Lin R, Mock L, Ngan I, Pack M, Stott G, Stout TJ, Yu P, Zaharia C, Zhang W, Zhou P, Nuss JM, Kearney PC, Xu W (2012) The design, synthesis, and biological evaluation of PIM kinase inhibitors. Bioorg Med Chem Lett 22:3732-3738
19. Giraud F, Akué-Gédu R, Nauton L, Candelon N, Debiton E, Théry V, Anizon F, Moreau P (2012) Synthesis and biological activities of 4-substituted pyrrolo[2,3-a]carbazole Pim kinase inhibitors. Eur J Med Chem 56:225-236
20. Pierre F, Regan CF, Chevrel M-C, Siddiqui-Jain A, Macalino D, Streiner N, Drygin D, Haddach M, O'Brien SE, Rice WG, Ryckman DM (2012) Novel potent dual inhibitors of CK2 and Pim kinases with antiproliferative activity against cancer cells. Bioorg Med Chem Lett 22(9):3327-3331
21. Catalyst 4.11 User Guide (2005) Accelrys Software Inc. San Diego
22. McCluskey A, Keller PA, Morgan J, Garner J (2003) Synthesis, molecular modeling and biological activity of methyl and thiomethyl substituted pyrimidines as corticotropin releasing hormone type 1 antagonists. Org Biomol Chem 1(19):3353-3361
23. Discovery Studio 4.1 user Guide (2010) Biovia (Accelrys) Software Inc. San Diego
24. Shahin R, AlQtaishat S, Taha M (2012) Elaborate ligand-based modeling reveal new submicromolar Rho kinase inhibitors. J Comput Aided Mol Des 26(2):249-266
25. Li H, Sutter J, Hoffmann R (2000) In: Güner OF (ed) Pharmacophore perception, development, and use in drug design. International University Line, La Jolla, pp 173-189
26. Sutter J, Guner O, Hoffmann R, Li H, Waldman M (2000) In: Guner OF (ed) Pharmacophore perception, development, and use in drug design. International University Line, La Jolla, pp 501-511
27. Kurogi Y, Guner OF (2001) Pharmacophore modeling and three-dimensional database searching for drug design using catalyst. Curr Med Chem 8(9):1035-1055
28. Bersuker I, Bahçeci S, Boggs J (2000) Pharmacophore perception, development and use in drug design. International University Line, La Jolla, pp 457-473
29. Abu Hammad AM, Taha MO (2009) Pharmacophore modeling, quantitative structure-activity relationship analysis, and shape-complemented in silico screening allow access to novel influenza neuraminidase inhibitors. J Chem Inf Model 49:978-996
30. Abu Khalaf R, Abu Sheikha G, Bustanji Y, Taha MO (2010) Discovery of new cholesteryl ester transfer protein inhibitors via ligand-based pharmacophore modeling and QSAR analysis followed by synthetic exploration. Eur J Med Chem 45(4):1598-1617
31. Abuhamdah S, Habash M, Taha MO (2013) Elaborate ligand-based modeling coupled with QSAR analysis and in silico screening reveal new potent acetylcholinesterase inhibitors. J Comput-Aided Mol Des 27(12):1075-1092
32. Al-Masri IM, Mohammad MK, Taha MO (2008) Discovery of DPP IV inhibitors by pharmacophore modeling and QSAR analysis followed by in silico screening. ChemMedChem 3(11):1763-1779
33. Taha MO, Bustanji Y, Al-Ghussein MAS, Mohammad M, Zalloum H, Al-Masri IM, Atallah N (2008) Pharmacophore modeling, quantitative structure-activity relationship analysis, and in silico screening reveal potent glycogen synthase kinase-3β inhibitory activities for cimetidine hydroxychloroquine, and gemifloxacin. J Med Chem 51(7):2062-2077
34. Taha MO, Qandil AM, Al-Haraznah T, Khalaf RA, Zalloum H, Al-Bakri AG (2011) Discovery of new antifungal leads via pharmacophore modeling and QSAR analysis of fungal N-myristoyl transferase inhibitors followed by in silico screening. Chem Biol Drug Des 78(3):391-407
35. Taha MO, Qandil AM, Zaki DD, AlDamen MA (2005) Ligand-based assessment of factor Xa binding site flexibility via elaborate pharmacophore exploration and genetic algorithm-based QSAR modeling. Eur J Med Chem 40(7):701-727
36. Poptodorov K, Luu T, Langer T, Hoffmann R (2006) Methods and principles in medicinal chemistry. In: Hoffmann RD (ed) Pharmacophores and pharmacophores searches, vol 2. Wiley, Weinheim, pp 17-47
37. Zheng W, Tropsha A (2000) Novel variable selection quantitative structure-property relationship approach based on the k-nearest-neighbor principle. J Chem Inf Comput Sci 40:185-194
38. Fischer R (1966) The principle of experimentation illustrated by a psycho-physical, chapter II, 8th edn. ExpeHafner Publishing Co., Hafner Publishing, New York
39. Shahin R, Taha MO (2012) Elaborate ligand-based modeling and subsequent synthetic exploration unveil new nanomolar Ca2+/calmodulin-dependent protein kinase II inhibitory leads. Bioorg Med Chem Lett 20(1):377-400
40. Taha MO, Atallah N, Al-Bakri AG, Paradis-Bleau C, Zalloum H, Younis KS, Levesque RC (2008) Discovery of new MurF inhibitors via pharmacophore modeling and QSAR analysis followed by in silico screening. Bioorg Med Chem 16(3):1218-1235
41. Taha MO, Bustanji Y, Al-Bakri AG, Yousef AM, Zalloum WA, Al-Masri IM, Atallah N (2007) Discovery of new potent human protein tyrosine phosphatase inhibitors via pharmacophore and QSAR analysis followed by in silico screening. J Mol Graph Model 25(6):870-884
42. Verdonk ML, Berdini V, Hartshorn MJ, Mooij WT, Murray CW, Taylor RD, Watson P (2004) Virtual screening using protein-ligand docking: avoiding artificial enrichment. J Chem Inf Comput Sci 44(3):793-806
43. Kirchmair J, Markt P, Distinto S, Wolber G, Langer T (2008) Evaluation of the performance of 3D virtual screening protocols: RMSD comparisons, enrichment assessments, and decoy selection-What can we learn from earlier mistakes? J Comput Aided Mol Des 22(3-4):213-228
44. Irwin JJ, Shoichet BK (2005) ZINC - a free database of commercially available compounds for virtual screening. J Chem Inf Model 45(1):177-182
45. Jacobsson M, Liden P, Fau-Stjernschantz E, Stjernschantz E, Fau-Bostrom H, Bostrom H, Fau-Norinder U, Norinder U (2003) J Med Chem 46:5781
46. Kirchmair J, Markt P, Distinto S, Schuster D, Spitzer GM, Liedl KR, Langer T, Wolber G (2008) The Protein Data Bank (PDB), its related services and software tools as key components for in silico guided drug discovery. J Med Chem. 51(22):7021-7040
47. Triballeau N, Acher F, Brabet I, Pin JP, Bertrand HOJ (2005) Virtual screening workflow development guided by the "receiver operating characteristic" curve approach. Application to high-throughput docking on metabotropic glutamate receptor subtype 4. Med Chem 48:2534
48. Lipinski CA, Lombardo F, Dominy BW, Feeney PJ (2001) Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Adv Drug Deliv Rev 46(1-3):3-26
49. Veber DF, Johnson S, Cheng HY, Smith BR, Ward KW, Kopple KD (2002) Molecular properties that influence the oral bioavailability of drug candidates. J Med Chem 45(12):2615-2623
50. Pim I kinase Assay Kit (Cat# CY-1167) (2009) CycLex, M., Ed. Ina Nagano, Japan
51. Güner O, Clement O, Kurogi Y (2004) Pharmacophore modeling and three dimensional database searching for drug design using catalyst recent advances. Curr Med Chem 11(22):2991-3005
52. Ramsey LF, Schafer WD (1997) The statistical sleuth, 1st edn. Wadsworth Publishing Company, Belmont
53. Fukui K (1982) The role of frontier orbitals in chemical reactions. Science 218(4574):747-754
54. Kikuchi O (1987) Systematic QSAR procedures with quantum chemical descriptors. Quant Struct Act Relatsh 6(4):179-184. doi: 10.1002/qsar.19870060406
55. Prasad YR, Kumar KR, Smiles J, Babu A (2008) QSAR studies on chalcone derivatives as antibacterial agents against Bacillus pumilis. Arkivoc 11:266-276. doi: 10.3998/ark.5550190.0009.b26
56. Bemis GW, Murcko MA (1996) The properties of known drugs 1. Molecular frameworks. J Med Chem 39:2887