Identification and in vitro evaluation of new leads as selective and competitive glycogen synthase kinase-3β inhibitors through ligand and structure based drug design

Journal of Molecular Graphics and Modelling

Volumn 53, Issue , 2014, Pages 31-47

  Darshit, B S ^a   Balaji, B ^a   Rani, P ^b   Ramanathan, M ^a  

^a PSG COLLEGE OF PHARMACY   (India)

^b PSG COLLEGE OF TECHNOLOGY   (India)

Author keywords

Cyclin dependent kinase 5 p25 (CDK5 p25); Glycogen synthase kinase 3 (GSK 3 ); Kinase assay; Ligand based drug design (LBDD); Structure based drug design (SBDD); Virtual screening

Indexed keywords

ASSAYS; CHAINS; DRUG DELIVERY; ENZYME INHIBITION; LIGANDS; MOLECULES; PHARMACODYNAMICS;

CYCLIN-DEPENDENT KINASE; DRUG DESIGN; GLYCOGEN SYNTHASE KINASE-3; KINASE ASSAYS; STRUCTURE BASED DRUG DESIGNS; VIRTUAL SCREENING;

STRUCTURAL DESIGN;

2,4 THIAZOLIDINEDIONE DERIVATIVE; ADENOSINE TRIPHOSPHATE; ARGININE; ASPARTIC ACID; BENZOTHIOPHENE; CYCLIN DEPENDENT KINASE 5; GLYCOGEN SYNTHASE KINASE 3 INHIBITOR; GLYCOGEN SYNTHASE KINASE 3BETA; IMIDAZO ISOQUINOLINE; ISOQUINOLINE; LYSINE; QUINAZOLINONE DERIVATIVE; TYROSINE; UNCLASSIFIED DRUG; VALINE; GLYCOGEN SYNTHASE KINASE 3; GLYCOGEN SYNTHASE KINASE 3 BETA; LIGAND; PROTEIN BINDING; PROTEIN KINASE INHIBITOR;

ARTICLE; BINDING AFFINITY; BINDING SITE; BIOLOGICAL ACTIVITY; CHEMICAL INTERACTION; CLINICAL EVALUATION; DRUG DESIGN; DRUG IDENTIFICATION; DRUG POTENCY; DRUG SCREENING; DRUG SELECTIVITY; ENZYME INHIBITION; ENZYME INHIBITION ASSAY; HUMAN; HUMAN CELL; HYDROGEN BOND; HYDROPHOBICITY; IC 50; IN VITRO STUDY; LIGAND BASED DRUG DESIGN; MOLECULAR DOCKING; PHARMACOPHORE; PRIORITY JOURNAL; QUANTITATIVE STRUCTURE ACTIVITY RELATION; STATIC ELECTRICITY; STRUCTURE BASED DRUG DESIGN; ANTAGONISTS AND INHIBITORS; CHEMICAL STRUCTURE; CHEMISTRY; COMPUTER SIMULATION; ENZYME ACTIVE SITE;

CATALYTIC DOMAIN; COMPUTER SIMULATION; DRUG DESIGN; GLYCOGEN SYNTHASE KINASE 3; HUMANS; HYDROGEN BONDING; LIGANDS; MODELS, MOLECULAR; PROTEIN BINDING; PROTEIN KINASE INHIBITORS; QUANTITATIVE STRUCTURE-ACTIVITY RELATIONSHIP;

EID: 84905004947     PISSN: 10933263     EISSN: 18734243     Source Type: Journal    
DOI: 10.1016/j.jmgm.2014.06.013     Document Type: Article

References (46)

1. J.R. Woodgett Molecular cloning and expression of glycogen synthase kinase-3/factor A EMBO J. 9 1990 2431 2438
2. M. Takahashi, K. Tomizawa, R. Kato, K. Sato, T. Uchida, S.C. Fujita, and K. Imahori Localization and developmental changes of tau protein kinase I/glycogen synthase kinase-3 beta in rat brain J. Neurochem. 63 1994 245 255 (Pubitemid 24184925)
3. G.N. Bijur, and R.S. Jope Glycogen synthase kinase-3 beta is highly activated in nuclei and mitochondria Neuroreport 14 2003 2415 2419
4. K. Hughes, E. Nikolakaki, S.E. Plyte, N.F. Totty, and J.R. Woodgett Modulation of the glycogen synthase kinase-3 family by tyrosine phosphorylation EMBO J. 12 1993 803 808 (Pubitemid 23073729)
5. C. Picton, J. Woodgett, B. Hemmings, and P. Cohen Multisite phosphorylation of glycogen synthase from rabbit skeletal muscle: phosphorylation of site 5 by glycogen synthase kinase-5 (casein kinase-II) is a prerequisite for phosphorylation of sites 3 by glycogen synthase kinase-3 FEBS Lett. 150 1982 191 196
6. A. Kannoji, S. Phukan, V. Sudher Babu, and V.N. Balaji GSK3beta: a master switch and a promising target Expert Opin. Ther. Targets 12 2008 1443 1455
7. M.P. Mazanetz, and P.M. Fischer Untangling tau hyperphosphorylation in drug design for neurodegenerative diseases Nat. Rev. Drug Discov. 6 2007 464 479 (Pubitemid 47064569)
8. D. Tang, and J.H. Wang Cyclin-dependent kinase 5 (Cdk5) and neuron-specific Cdk5 activators Prog. Cell Cycle Res. 2 1996 205 216
9. S. Cicero, and K. Herrup Cyclin-dependent kinase 5 is essential for neuronal cell cycle arrest and differentiation J. Neurosci. 25 2005 9658 9668 (Pubitemid 41510906)
10. F. Causeret, T. Jacobs, M. Terao, O. Heath, M. Hoshino, and M. Nikolic Neurabin-I is phosphorylated by Cdk5: implications for neuronal morphogenesis and cortical migration Mol. Biol. Cell 18 2007 4327 4342 (Pubitemid 350060162)
11. T. Ohshima, E.C. Gilmore, G. Longenecker, D.M. Jacobowitz, R.O. Brady, K. Herrup, and A.B. Kulkarni Migration defects of cdk5(-/-) neurons in the developing cerebellum is cell autonomous J. Neurosci. 19 1999 6017 6026 (Pubitemid 29327935)
12. V. Stambolic, L. Ruel, and J.R. Woodgett Lithium inhibits glycogen synthase kinase-3 activity and mimics wingless signalling in intact cells Curr. Biol. 6 1996 1664 1668 (Pubitemid 27050234)
13. L. Meijer, M. Flajolet, and P. Greengard Pharmacological inhibitors of glycogen synthase kinase 3 Trends Pharmacol. Sci. 25 2004 471 480 (Pubitemid 39149703)
14. A. Martinez, M. Alonso, A. Castro, C. Pérez, and F.J. Moreno First non-ATP competitive glycogen synthase kinase 3 beta (GSK-3beta) inhibitors: thiadiazolidinones (TDZD) as potential drugs for the treatment of Alzheimer's disease J. Med. Chem. 45 2002 1292 1299 (Pubitemid 34263565)
15. M. Hamann, D. Alonso, E. Martín-Aparicio, A. Fuertes, M.J. Pérez-Puerto, A. Castro, S. Morales, M.L. Navarro, M. Del Monte-Millán, M. Medina, H. Pennaka, A. Balaiah, J. Peng, J. Cook, S. Wahyuono, and A. Martínez Glycogen synthase kinase-3 (GSK-3) inhibitory activity and structure-activity relationship (SAR) studies of the manzamine alkaloids. Potential for Alzheimer's disease J. Nat. Prod. 70 2007 1397 1405 (Pubitemid 47584577)
16. S. Conde, D.I. Pérez, A. Martínez, C. Perez, and F.J. Moreno Thienyl and phenyl alpha-halomethyl ketones: new inhibitors of glycogen synthase kinase (GSK-3beta) from a library of compound searching J. Med. Chem. 46 2003 4631 4633 (Pubitemid 37271611)
17. S. Phukan, V.S. Babu, A. Kannoji, R. Hariharan, and V.N. Balaji GSK3beta: role in therapeutic landscape and development of modulators Br. J. Pharmacol. 160 2010 1 19
18. D. Wei, X. Jiang, L. Zhou, J. Chen, Z. Chen, C. He, K. Yang, Y. Liu, J. Pei, and L. Lai Discovery of multitarget inhibitors by combining molecular docking with common pharmacophore matching J. Med. Chem. 51 2008 7882 7888
19. S.H. Lu, J.W. Wu, H.L. Liu, J.H. Zhao, K.T. Liu, C.K. Chuang, H.Y. Lin, W.B. Tsai, and Y. Ho The discovery of potential acetylcholinesterase inhibitors: a combination of pharmacophore modeling, virtual screening, and molecular docking studies J. Biomed. Sci. 18 2011 8 20
20. F.X. Tavares, J.A. Boucheron, S.H. Dickerson, R.J. Griffin, F. Preugschat, S.A. Thomson, T.Y. Wang, and H.Q. Zhou N-phenyl-4-pyrazolo[1,5-b] pyridazin-3-ylpyrimidin-2-amines as potent and selective inhibitors of glycogen synthase kinase 3 with good cellular efficacy J. Med. Chem. 47 2004 4716 4730 (Pubitemid 39195562)
21. P. Polychronopoulos, P. Magiatis, A.L. Skaltsounis, V. Myrianthopoulos, E. Mikros, A. Tarricone, A. Musacchio, S.M. Roe, L. Pearl, M. Leost, P. Greengard, and L. Meijer Structural basis for the synthesis of indirubins as potent and selective inhibitors of glycogen synthase kinase-3 and cyclin-dependent kinases J. Med. Chem. 47 2004 935 946 (Pubitemid 38176796)
22. M. Saitoh, J. Kunitomo, E. Kimura, H. Iwashita, Y. Uno, T. Onishi, N. Uchiyama, T. Kawamoto, T. Tanaka, C.D. Mol, D.R. Dougan, G.P. Textor, G.P. Snell, M. Takizawa, F. Itoh, and M. Kori 2-{3-[4-(Alkylsulfinyl)phenyl]-1- benzofuran-5-yl}-5-methyl-1,3,4-oxadiazole derivatives as novel inhibitors of glycogen synthase kinase-3beta with good brain permeability J. Med. Chem. 52 2009 6270 6286
23. Maestro Version 9.0, Schrödinger 2010 LLC New York, NY
24. LigPrep Version 2.3, Schrödinger 2010 LLC New York, NY
25. U.A. Shah, H.S. Deokar, S.S. Kadam, and V.M. Kulkarni Pharmacophore generation and atom-based 3D-QSAR of novel 2-(4-methylsulfonylphenyl)pyrimidines as COX-2 inhibitors Mol. Divers. 14 2010 559 568
26. Y. Li, Y. Wang, and F. Zhang Pharmacophore modeling and 3D-QSAR analysis of phosphoinositide 3-kinase p110alpha inhibitors J. Mol. Model. 16 2010 1449 1460
27. Phase Version 3.2, Schrödinger 2010 LLC New York, NY
28. S.L. Dixon, A.M. Smondyrev, E.H. Knoll, S.N. Rao, D.E. Shaw, and R.A. Friesner PHASE: a new engine for pharmacophore perception, 3D QSAR model development, and 3D database screening: 1. Methodology and preliminary results J. Comput. Aided Mol. Des. 20 2006 647 671 (Pubitemid 46023928)
29. R. Bhat, Y. Xue, S. Berg, S. Hellberg, M. Ormö, Y. Nilsson, A.C. Radesäter, E. Jerning, P.O. Markgren, T. Borgegård, M. Nylöf, A. Giménez-Cassina, F. Hernández, J.J. Lucas, J. Díaz-Nido, and J. Avila Structural insights and biological effects of glycogen synthase kinase 3-specific inhibitor AR-A014418 J. Biol. Chem. 278 2003 45937 45945 (Pubitemid 37432740)
30. M. Mapelli, L. Massimiliano, C. Crovace, M.A. Seeliger, L.H. Tsai, L. Meijer, and A. Musacchio Mechanism of CDK5/p25 binding by CDK inhibitors J. Med. Chem. 48 2005 671 679 (Pubitemid 40209090)
31. Glide Version 5.6, Schrödinger 2010 LLC New York, NY
32. A. Baki, A. Bielik, L. Molnár, G. Szendrei, and G.M. Keserü A high throughput luminescent assay for glycogen synthase kinase-3beta inhibitors Assay Drug Dev. Technol. 5 2007 75 83 (Pubitemid 46581242)
33. S.L. Dixon, A.M. Smondyrev, and S.N. Rao PHASE: a novel approach to pharmacophore modeling and 3D database searching Chem. Biol. Drug Des. 67 2006 370 372
34. R.P. Verma, and C. Hansch QSAR modeling of taxane analogues against colon cancer Eur. J. Med. Chem. 45 2010 1470 1477
35. A. Golbraikh, and A. Tropsha Beware of q2! J. Mol. Graph. Model. 20 2002 269 276
36. B. Balaji, R. Muthiah, R. Sabarinath, and Chandrasekharan Descriptor analysis of estrogen receptor β-selective ligands using 2-phenylquinoline, tetrahydrofluorenone and 3-hydroxy 6H-benzo[c]chromen-6-one scaffolds J. Enzyme Inhib. Med. Chem. 26 2011 831 842
37. J.H. Van Drie Pharmacophore discovery - lessons learned Curr. Pharm. Des. 91 2003 649 1664
38. N. Dessalew, and P.V. Bharatam Identification of potential glycogen kinase-3 inhibitors by structure based virtual screening Biophys. Chem. 128 2007 165 175 (Pubitemid 46860305)
39. H.J. Kim, H. Choo, Y.S. Cho, K.T. No, and A.N. Pae Novel GSK-3beta inhibitors from sequential virtual screening Bioorg. Med. Chem. 16 2008 636 643 (Pubitemid 351163074)
40. D.I. Osolodkin, V.A. Palyulin, and N.S. Zefirov Structure-based virtual screening of glycogen synthase kinase 3β inhibitors: analysis of scoring functions applied to large true actives and decoy sets Chem. Biol. Drug Des. 78 2011 378 390
41. L. Feng, Y. Geisselbrecht, S. Blanck, A. Wilbuer, G.E. Atilla-Gokcumen, P. Filippakopoulos, K. Kräling, M.A. Celik, K. Harms, J. Maksimoska, R. Marmorstein, G. Frenking, S. Knapp, L.O. Essen, and E. Meggers Structurally sophisticated octahedral metal complexes as highly selective protein kinase inhibitors J. Am. Chem. Soc. 20 2011 5976 5986
42. C. Logé, A. Testard, V. Thiéry, O. Lozach, M. Blairvacq, J.M. Robert, L. Meijer, and T. Besson Novel 9-oxo-thiazolo[5,4-f]quinazoline-2- carbonitrile derivatives as dual cyclin-dependent kinase 1 (CDK1)/glycogen synthase kinase-3 (GSK-3) inhibitors: synthesis, biological evaluation and molecular modeling studies Eur. J. Med. Chem. 43 2008 1469 1477 (Pubitemid 351890437)
43. M. Arnost, A. Pierce, E. Haar, D. Lauffer, J. Madden, K. Tanner, and J. Green 3-Aryl-4-(arylhydrazono)-1H-pyrazol-5-ones: highly ligand efficient and potent inhibitors of GSK3beta Bioorg. Med. Chem. Lett. 20 2010 1661 1664
44. V. Pande, and M.J. Ramos Structural basis for the GSK-3beta binding affinity and selectivity against CDK-2 of 1-(4-aminofurazan-3yl)-5- dialkylaminomethyl-1H-[1-3] triazole-4-carboxylic acid derivatives Bioorg. Med. Chem. Lett. 15 2005 5129 5135 (Pubitemid 41463633)
45. T. Kramer, B. Schmidt, and F.L. Monte Small-molecule inhibitors of GSK-3: structural insights and their application to Alzheimer's disease models Int. J. Alzheimers Dis. 2012 2012 1 32
46. N. Zhang, Y.J. Jiang, Q.S. Yu, and J.W. Zou Studies of glycogen synthase kinase-3 inhibitors Prog. Chem. 19 2007 614 623