E-pharmacophore-based virtual screening to identify GSK-3β inhibitors

References

• Sivaprakasam K. Towards a unifying hypothesis of Alzheimer’s disease: cholinergic system linked to plaques, tangles and neuroinflammation. Curr Med Chem 2006;13:2179–88
   PubMed Web of Science ®Google Scholar
• Jope RS, Johnson GV. The glamour and gloom of glycogen synthase kinase-3. Trends Biochem Sci 2004;29:95–102
   PubMed Web of Science ®Google Scholar
• Thotala DK, Hallahan DE, Yazlovitskaya EM. Glycogen synthase kinase 3β inhibitors protect hippocampal neurons from radiation-induced apoptosis by regulating MDM2-p53 pathway. Cell Death Differ 2012;19:387–96
   PubMed Web of Science ®Google Scholar
• Cohen P, Frame S. The renaissance of GSK3. Nat Rev Mol Cell Biol 2001;2:769–76
   PubMed Web of Science ®Google Scholar
• Agarwal-Mawal A, Qureshi HY, Cafferty PW, et al. 14-3-3 connects glycogen synthase kinase-3 beta to tau within a brain microtubule-associated tau phosphorylation complex. J Biol Chem 2003;278:12722–8
   PubMed Web of Science ®Google Scholar
• Cho JH, Johnson GV. Glycogen synthase kinase 3beta phosphorylates tau at both primed and unprimed sites. Differential impact on microtubule binding. J Biol Chem 2003;278:187–93
   PubMed Web of Science ®Google Scholar
• Hernández F, Avila J. The role of glycogen synthase kinase 3 in the early stages of Alzheimers’ disease. FEBS Lett 2008;582:3848–54
   PubMed Web of Science ®Google Scholar
• Bhat RV, Budd Haeberlein SL, Avila J. Glycogen synthase kinase 3: a drug target for CNS therapies. J Neurochem 2004;89:1313–17
   PubMed Web of Science ®Google Scholar
• Fulga TA, Elson-Schwab I, Khurana V, et al. Abnormal bundling and accumulation of F-actin mediates tau-induced neuronal degeneration in vivo. Nat Cell Biol 2007;9:139–48
   PubMed Web of Science ®Google Scholar
• Cohen P, Goedert M. GSK3 inhibitors: development and therapeutic potential. Nat Rev Drug Discov 2004;3:479–87
   PubMed Web of Science ®Google Scholar
• Emamian ES, Hall D, Birnbaum MJ, et al. Convergent evidence for impaired AKT1-GSK3beta signaling in schizophrenia. Nat Genet 2004;36:131–7
   PubMed Web of Science ®Google Scholar
• Hanger DP, Hughes K, Woodgett JR, et al. Glycogen synthase kinase-3 induces Alzheimer’s disease-like phosphorylation of tau: generation of paired helical filament epitopes and neuronal localisation of the kinase. Neurosci Lett 1992;147:58–62
   PubMed Web of Science ®Google Scholar
• Martin L, Magnaudeix A, Esclaire F, et al. Inhibition of glycogen synthase kinase-3beta downregulates total tau proteins in cultured neurons and its reversal by the blockade of protein phosphatase-2A. Brain Res 2009;1252:66–75
   PubMed Web of Science ®Google Scholar
• Goldbaum O, Richter-Landsberg C. Activation of PP2A-like phosphatase and modulation of tau phosphorylation accompany stress-induced apoptosis in cultured oligodendrocytes. Glia 2002;40:271–82
   PubMed Web of Science ®Google Scholar
• Kihira T, Suzuki A, Kondo T, et al. Immunohistochemical expression of IGF-I and GSK in the spinal cord of Kii and Guamanian ALS patients. Neuropathology 2009;29:548–58
   PubMed Web of Science ®Google Scholar
• Martins DF, Rosa AO, Gadotti VM, et al. The antinociceptive effects of AR-A014418, a selective inhibitor of glycogen synthase kinase-3 beta, in mice. J Pain 2011;12:315–22
   PubMed Web of Science ®Google Scholar
• Tang Z, Arjunan P, Lee C, et al. Survival effect of PDGF-CC rescues neurons from apoptosis in both brain and retina by regulating GSK3beta phosphorylation. J Exp Med 2010;207:867–80
   PubMed Web of Science ®Google Scholar
• Castro A, Encinas A, Gil C, et al. Non-ATP competitive glycogen synthase kinase 3beta (GSK-3beta) inhibitors: study of structural requirements for thiadiazolidinone derivatives. Bioorg Med Chem 2008;16:495–510
   PubMed Web of Science ®Google Scholar
• Ciani L, Salinas PC. WNTs in the vertebrate nervous system: from patterning to neuronal connectivity. Nat Rev Neurosci 2005;6:351–62
   PubMed Web of Science ®Google Scholar
• Watcharasit P, Bijur GN, Song L, et al. Glycogen synthase kinase-3beta (GSK3beta) binds to and promotes the actions of p53. J Biol Chem 2003;278:48872–9
   PubMed Web of Science ®Google Scholar
• Thotala DK, Hallahan DE, Yazlovitskaya EM. Inhibition of glycogen synthase kinase 3 beta attenuates neurocognitive dysfunction resulting from cranial irradiation. Cancer Res 2008;68:5859–68
   PubMed Web of Science ®Google Scholar
• Yazlovitskaya EM, Edwards E, Thotala D, et al. Lithium treatment prevents neurocognitive deficit resulting from cranial irradiation. Cancer Res 2006;66:11179–86
   PubMed Web of Science ®Google Scholar
• Cross DA, Culbert AA, Chalmers KA, et al. Selective small-molecule inhibitors of glycogen synthase kinase-3 activity protect primary neurones from death. J Neurochem 2001;77:94–102
   PubMed Web of Science ®Google Scholar
• Ly PTT, Wu Y, Zou H, et al. Inhibition of GSK3β-mediated BACE1 expression reduces Alzheimer-associated phenotypes. J Clin Invest 2013;123:224–35
   PubMed Web of Science ®Google Scholar
• Leost M, Schultz C, Link A, et al. Paullones are potent inhibitors of glycogen synthase kinase-3beta and cyclin-dependent kinase 5/p25. Eur J Biochem 2000;267:5983–94
   PubMedGoogle Scholar
• Meijer L, Skaltsounis AL, Magiatis P, et al. GSK-3-selective inhibitors derived from Tyrian purple indirubins. Chem Biol 2003;10:1255–66
   PubMed Web of Science ®Google Scholar
• Engler TA, Malhotra S, Burkholder TP, et al. The development of potent and selective bisarylmaleimide GSK3 inhibitors. Bioorg Med Chem Lett 2005;15:899–903
   PubMed Web of Science ®Google Scholar
• Smith DG, Buffet M, Fenwick AE, et al. 3-Anilino-4-arylmaleimides: potent and selective inhibitors of glycogen synthase kinase-3 (GSK-3). Bioorg Med Chem Lett 2001;11:635–9
   PubMed Web of Science ®Google Scholar
• Zhang HC, White KB, Ye H, et al. Macrocyclic bisindolylmaleimides as inhibitors of protein kinase C and glycogen synthase kinase-3. Bioorg Med Chem Lett 2003;13:3049–53
   PubMed Web of Science ®Google Scholar
• Kuo GH, Prouty C, DeAngelis A, et al. Synthesis and discovery of macrocyclic polyoxygenated bis-7-azaindolylmaleimides as a novel series of potent and highly selective glycogen synthase kinase-3beta inhibitors. J Med Chem 2003;46:4021–31
   PubMed Web of Science ®Google Scholar
• Dessalew N, Bharatam PV. Investigation of potential glycogen synthase kinase 3 inhibitors using pharmacophore mapping and virtual screening. Chem Biol Drug Des 2006;68:154–65
   PubMed Web of Science ®Google Scholar
• Chu Y, Tsai K, Ye D, Li M. Modeling the Interaction between Glycogen Synthase Kinase 3 β (GSK-3β) and its Non-ATP competitive inhibitors [OL]. [2009-09-276:54:14]. http://www.paper.edu.cn/index.php/default/en_releasepaper/downPaper/200909-731
   Google Scholar
• Pradeep N, Munikumar M, Swargam S, et al. 197 Combination of e-pharmacophore modeling, multiple docking strategies and molecular dynamic simulations to discover of novel antagonists of BACE1. J Biomol Struct Dyn 2015;33:129–30
   PubMed Web of Science ®Google Scholar
• Pradhan D, Priyadarshini V, Aggrawal S, et al. 181 Discovery of potential inhibitors of BMX non-receptor tyrosine kinase through e-pharmacophore based virtual screening. J Biomol Struct Dyn 2015;33:118–20
   PubMed Web of Science ®Google Scholar
• Palakurti R, Sriram D, Yogeeswari P, Vadrevu R. Multiple e-pharmacophore modeling combined with high-throughput virtual screening and docking to identify potential inhibitors of β-Secretase (BACE1). Mol Inform 2013;32:385–98
   PubMed Web of Science ®Google Scholar
• Berman HM, Westbrook J, Feng Z, et al. The protein data bank. Nucleic Acids Res 2000;28:235–42
   PubMed Web of Science ®Google Scholar
• De Beer TA, Berka K, Thornton JM, Laskowski RA. PDBsum additions. Nucleic Acids Res 2014;42:D292–6
   Google Scholar
• Suvannang N, Nantasenamat C, Isarankura-Na-Ayudhya C, Prachayasittikul V. Molecular docking of aromatase inhibitors. Molecules 2011;16:3597–617
   Web of Science ®Google Scholar
• Chen J, Lai L. Pocket v.2: further developments on receptor-based pharmacophore modeling. J Chem Inf Model 2006;46:2684–91
   PubMed Web of Science ®Google Scholar
• Friesner RA, Banks JL, Murphy RB, et al. Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. J Med Chem 2004;47:1739–49
   PubMed Web of Science ®Google Scholar
• Bajaj R, Sharma V, Kumar V. Pharmacophore mapping: prediction of BCR–ABL kinase inhibitory activity of α-benzylthio chalcones. Bull Fac Pharm Cairo Univ 2014;52:103–8
   Google Scholar
• Muthusamy K, Singh KD, Chinnasamy S, et al. High throughput virtual screening and E-pharmacophore filtering in the discovery of new BACE-1 inhibitors. Interdiscip Sci 2013;5:119–26
   PubMed Web of Science ®Google Scholar
• Toledo Warshaviak D, Golan G, Borrelli KW, et al. Structure-based virtual screening approach for discovery of covalently bound ligands. J Chem Inf Model 2014;54:1941–50
   PubMed Web of Science ®Google Scholar
• Priyadarshini V, Pradhan D, Munikumar M, et al. Genome-based approaches to develop epitope-driven subunit vaccines against pathogens of infective endocarditis. J Biomol Struct Dyn 2014;32:876–89
   PubMed Web of Science ®Google Scholar
• Venkatraman V, Pérez-Nueno VI, Mavridis L, Ritchie DW. Comprehensive comparison of ligand-based virtual screening tools against the DUD data set reveals limitations of current 3D methods. J Chem Inf Model 2010;50:2079–93
   PubMed Web of Science ®Google Scholar
• Pradhan D, Priyadarshini V, Munikumar M, et al. Para-(benzoyl)-phenylalanine as a potential inhibitor against LpxC of Leptospira spp.: homology modeling, docking, and molecular dynamics study. J Biomol Struct Dyn 2014;32:171–85
   PubMed Web of Science ®Google Scholar
• Du J, Sun H, Xi L, et al. Molecular modeling study of checkpoint kinase 1 inhibitors by multiple docking strategies and prime/MM-GBSA calculation. J Comput Chem 2011;32:2800–9
   PubMed Web of Science ®Google Scholar
• Maestro 9.8, Schrodinger, New York, USA
   Google Scholar
• Brooks WH, Daniel KG, Sung S-S, Guida WC. Computational validation of the importance of absolute stereochemistry in virtual screening. J Chem Inf Model 2008;48:639–45
   PubMed Web of Science ®Google Scholar
• Greenwood JR, Calkins D, Sullivan AP, Shelley JC. Towards the comprehensive, rapid, and accurate prediction of the favorable tautomeric states of drug-like molecules in aqueous solution. J Comput Aided Mol Des 2010;24:591–604
   PubMed Web of Science ®Google Scholar
• Lipinski C, Hopkins A. Navigating chemical space for biology and medicine. Nature 2004;432:855–61
   PubMed Web of Science ®Google Scholar
• Friesner RA, Murphy RB, Repasky MP, et al. Extra precision glide: docking and scoring incorporating a model of hydrophobic enclosure for protein-ligand complexes. J Med Chem 2006;49:6177–96
   PubMed Web of Science ®Google Scholar
• Cho AE, Guallar V, Berne BJ, Friesner R. Importance of accurate charges in molecular docking: quantum mechanical/molecular mechanical (QM/MM) approach. J Comput Chem 2005;26:915–31
   PubMed Web of Science ®Google Scholar
• Wang H, Aslanian R, Madison VS. Induced-fit docking of mometasone furoate and further evidence for glucocorticoid receptor 17alpha pocket flexibility. J Mol Graph Model 2008;27:512–21
   PubMed Web of Science ®Google Scholar
• Klebe G, Krämer O, Sotriffer C. Strategies for the design of inhibitors of aldose reductase, an enzyme showing pronounced induced-fit adaptations. Cell Mol Life Sci 2004;61:783–93
   PubMed Web of Science ®Google Scholar
• Umamaheswari A, Kumar MM, Pradhan D, Marisetty H. Docking studies towards exploring antiviral compounds against envelope protein of yellow fever virus. Interdiscip Sci 2011;3:64–77
   PubMed Web of Science ®Google Scholar
• Amineni U, Pradhan D, Marisetty H. In silico identification of common putative drug targets in Leptospira interrogans. J Chem Biol 2010;3:165–73
   PubMedGoogle Scholar
• Das D, Koh Y, Tojo Y, et al. Prediction of potency of protease inhibitors using free energy simulations with polarizable quantum mechanics-based ligand charges and a hybrid water model. J Chem Inf Model 2009;49:2851–62
   PubMed Web of Science ®Google Scholar
• Lyne PD, Lamb ML, Saeh JC. Accurate prediction of the relative potencies of members of a series of kinase inhibitors using molecular docking and MM-GBSA scoring. J Med Chem 2006;49:4805–8
   PubMed Web of Science ®Google Scholar
• Maragakis P, Lindorff-Larsen K, Eastwood MP, et al. Microsecond molecular dynamics simulation shows effect of slow loop dynamics on backbone amide order parameters of proteins. J Phys Chem B 2008;112:6155–8
   PubMed Web of Science ®Google Scholar
• Jorgensen WL, Maxwell DS, Tirado-Rives J. Development and testing of the OPLS all-atom force field on conformational energetics and properties of organic liquids. J Am Chem Soc 1996;7863:11225–36
   Web of Science ®Google Scholar
• Kaminski GA, Friesner RA, Tirado-Rives J, Jorgensen WL. Evaluation and reparametrization of the OPLS-AA force field for proteins via comparison with accurate quantum chemical calculations on peptides. J Phys Chem B 2001;105:6474–87
   Web of Science ®Google Scholar
• Hayes JM, Skamnaki VT, Archontis G, et al. Kinetics, in silico docking, molecular dynamics, and MM-GBSA binding studies on prototype indirubins, KT5720, and staurosporine as phosphorylase kinase ATP-binding site inhibitors: the role of water molecules examined. Proteins 2011;79:703–19
   PubMed Web of Science ®Google Scholar
• Shan Y, Kim ET, Eastwood MP, et al. How does a drug molecule find its target binding site? J Am Chem Soc 2011;133:9181–3
   PubMed Web of Science ®Google Scholar
• Vilar S, Karpiak J, Berk B, Costanzi S. In silico analysis of the binding of agonists and blockers to the β2-adrenergic receptor. J Mol Graph Model 2011;29:809–17
   PubMed Web of Science ®Google Scholar
• Leimkuhler BJ, Sweet CR. The canonical ensemble via symplectic integrators using Nosé and Nosé-Poincaré chains. J Chem Phys 2004;121:108–16
   PubMed Web of Science ®Google Scholar
• Martyna GJ, Tobias DJ, Klein ML. Constant pressure molecular dynamics algorithms. J Chem Phys 1994;101:4177–89
   Web of Science ®Google Scholar
• Therese PJ, Manvar D, Kondepudi S, et al. Multiple e-pharmacophore modeling, 3D-QSAR, and high-throughput virtual screening of hepatitis C virus NS5B polymerase inhibitors. J Chem Inf Model 2014;54:539–52
   PubMed Web of Science ®Google Scholar
• Truchon JF, Bayly CI. Evaluating virtual screening methods: good and bad metrics for the “early recognition” problem. J Chem Inf Model 2007;47:488–508
   PubMed Web of Science ®Google Scholar
• Yang CY, Sun H, Chen J, et al. Importance of ligand reorganization free energy in protein-ligand binding-affinity prediction. J Am Chem Soc 2009;131:13709–21
   PubMed Web of Science ®Google Scholar
• Gilson MK, Zhou HX. Calculation of protein-ligand binding affinities. Annu Rev Biophys Biomol Struct 2007;36:21–42
   PubMedGoogle Scholar
• Zhang B, Tan VB, Lim KM, et al. Study of the inhibition of cyclin-dependent kinases with roscovitine and indirubin-3'-oxime from molecular dynamics simulations. J Mol Model 2007;13:79–89
   PubMed Web of Science ®Google Scholar
• Barillari C, Taylor J, Viner R, Essex JW. Classification of water molecules in protein binding sites. J Am Chem Soc 2007;129:2577–87
   PubMed Web of Science ®Google Scholar
• Poornima CS, Dean PM. Hydration in drug design. 1. Multiple hydrogen-bonding features of water molecules in mediating protein-ligand interactions. J Comput Aided Mol Des 1995;9:500–12
   PubMed Web of Science ®Google Scholar
• Valiev M, Yang J, Adams JA, et al. Phosphorylation reaction in cAPK protein kinase-free energy quantum mechanical/molecular mechanics simulations. J Phys Chem B 2007;111:13455–64
   PubMed Web of Science ®Google Scholar