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Letters in Drug Design & Discovery

Editor-in-Chief

ISSN (Print): 1570-1808
ISSN (Online): 1875-628X

Research Article

In Silico Studies to Develop New GSK3β Inhibitors Effective in the Alzheimer's Disease

Author(s): Gozde Yalcin Ozkat* and Ilkay Yildiz

Volume 19, Issue 8, 2022

Published on: 14 March, 2022

Page: [691 - 705] Pages: 15

DOI: 10.2174/1570180819666220210100813

Price: $65

Abstract

Background: Alzheimer's disease affects a large part of the world’s population by prolonging the human life span and becoming an economic burden in the health system. Therefore, its treatment becomes more and more important every day. With the insufficiency of existing drug molecules, new drug targets are being searched. The most important of these is the Glycogen Synthase Kinase 3β enzyme, which is thought to be of key importance in Tau hyperphosphorylation and Amyloid β accumulation mechanisms.

Objective: In this research, computational studies were conducted to develop a new GSK3β enzyme inhibitor.

Methods: Leading compounds suitable for pharmacophore models obtained by the 3D QSAR method were scanned in databases. In silico ADME/Tox analyses were performed on the obtained molecules.

Results: Although the three molecules (ENA99104, CNR13756, TIM405938) had strong Dock Scores (42.869, 53.344, and 41.119, respectively) in molecular docking calculations, only the CNR13756 molecule was found successful according to molecular dynamics simulations.

Conclusion: All computational studies have revealed that the CNR13756 molecule can exhibit a therapeutic scaffold property, thus obtaining a selective GSK3β inhibitor with minimal side effects

Keywords: Molecular docking, LigandFit, QSAR, molecular dynamics simulations, AMBER14, in silico ADME/Tox analysis, pharmacophore modeling.

Graphical Abstract

[1]
Huang, L.K.; Chao, S.P.; Hu, C.J. Clinical trials of new drugs for Alzheimer disease. J. Biomed. Sci., 2020, 27(1), 18.
[http://dx.doi.org/10.1186/s12929-019-0609-7] [PMID: 31906949]
[2]
Xu, Y.; Yan, J.; Zhou, P.; Li, J.; Gao, H.; Xia, Y.; Wang, Q. Neurotransmitter receptors and cognitive dysfunction in Alzheimer’s disease and Parkinson’s disease. Prog. Neurobiol., 2012, 97(1), 1-13.
[http://dx.doi.org/10.1016/j.pneurobio.2012.02.002] [PMID: 22387368]
[3]
Ohno, M.; Sametsky, E.A.; Younkin, L.H.; Oakley, H.; Younkin, S.G.; Citron, M.; Vassar, R.; Disterhoft, J.F. BACE1 deficiency rescues memory deficits and cholinergic dysfunction in a mouse model of Alzheimer’s disease. Neuron, 2004, 41(1), 27-33.
[http://dx.doi.org/10.1016/S0896-6273(03)00810-9] [PMID: 14715132]
[4]
He, Z.; Guo, J.L.; McBride, J.D.; Narasimhan, S.; Kim, H.; Changolkar, L.; Zhang, B.; Gathagan, R.J.; Yue, C.; Dengler, C.; Stieber, A.; Nitla, M.; Coulter, D.A.; Abel, T.; Brunden, K.R.; Trojanowski, J.Q.; Lee, V.M.Y. Amyloid-β plaques enhance Alzheimer’s brain tau-seeded pathologies by facilitating neuritic plaque tau aggregation. Nat. Med., 2018, 24(1), 29-38.
[http://dx.doi.org/10.1038/nm.4443] [PMID: 29200205]
[5]
Vassar, R.; Bennett, B.D.; Babu-Khan, S.; Kahn, S.; Mendiaz, E.A.; Denis, P.; Teplow, D.B.; Ross, S.; Amarante, P.; Loeloff, R.; Luo, Y.; Fisher, S.; Fuller, J.; Edenson, S.; Lile, J.; Jarosinski, M.A.; Biere, A.L.; Curran, E.; Burgess, T.; Louis, J.C.; Collins, F.; Treanor, J.; Rogers, G.; Citron, M. Be-ta-secretase cleavage of Alzheimer’s amyloid precursor protein by the transmembrane aspartic protease BACE. Science, 1999, 286, 735.
[6]
Hooper, C.; Killick, R.; Lovestone, S. The GSK3 hypothesis of Alzheimer’s disease. J. Neurochem., 2008, 104(6), 1433-1439.
[http://dx.doi.org/10.1111/j.1471-4159.2007.05194.x] [PMID: 18088381]
[7]
Gong, C.X.; Iqbal, K. Hyperphosphorylation of microtubule-associated protein tau: A promising therapeutic target for Alzheimer disease. Curr. Med. Chem., 2008, 15(23), 2321-2328.
[http://dx.doi.org/10.2174/092986708785909111] [PMID: 18855662]
[8]
Aisen, P.S.; Cummings, J.; Schneider, L.S. Symptomatic and nonamyloid/tau based pharmacologic treatment for Alzheimer disease. Cold Spring Harb. Perspect. Med., 2012, 2(3), a006395.
[http://dx.doi.org/10.1101/cshperspect.a006395] [PMID: 22393531]
[9]
Namrata, C. Case study-Alzheimer’s disease., 2012. Availale from: http://www.namrata.co/case-study-alzheimer-disease/
[10]
Zhang, Y.W.; Thompson, R.; Zhang, H.; Xu, H. APP processing in Alzheimer’s disease. Mol. Brain, 2011, 4, 3.
[http://dx.doi.org/10.1186/1756-6606-4-3] [PMID: 21214928]
[11]
Lee, S.J.; Chung, Y.H.; Joo, K.M.; Lim, H.C.; Jeon, G.S.; Kim, D.; Lee, W.B.; Kim, Y.S.; Cha, C.I. Age-related changes in glycogen syn-thase kinase 3β (GSK3β) immunoreactivity in the central nervous system of rats. Neurosci. Lett., 2006, 409(2), 134-139.
[http://dx.doi.org/10.1016/j.neulet.2006.09.026] [PMID: 17046157]
[12]
Leroy, K.; Yilmaz, Z.; Brion, J.P. Increased level of active GSK-3β in Alzheimer’s disease and accumulation in argyrophilic grains and in neurones at different stages of neurofibrillary degeneration. Neuropathol. Appl. Neurobiol., 2007, 33(1), 43-55.
[http://dx.doi.org/10.1111/j.1365-2990.2006.00795.x] [PMID: 17239007]
[13]
Lauretti, E.; Dincer, O.; Praticò, D. Glycogen synthase kinase-3 signaling in Alzheimer’s disease. Biochim. Biophys. Acta Mol. Cell Res., 2020, 1867(5), 118664.
[http://dx.doi.org/10.1016/j.bbamcr.2020.118664] [PMID: 32006534]
[14]
Yilmaz, S.; Ataei, S.; Yildiz, I. Molecular docking studies on some benzamide derivatives as topoisomerase inhibitors. Ankara Univ Eczac Fak Derg., 2020, 44, 470-480.
[http://dx.doi.org/10.33483/jfpau.789537]
[15]
Hansson, T.; Oostenbrink, C.; van Gunsteren, W. Molecular dynamics simulations. Curr. Opin. Struct. Biol., 2002, 12(2), 190-196.
[http://dx.doi.org/10.1016/S0959-440X(02)00308-1] [PMID: 11959496]
[16]
Salmaso, V.; Moro, S. Bridging molecular docking to molecular dynamics in exploring ligand-protein recognition process: An overview. Front. Pharmacol., 2018, 9, 923.
[http://dx.doi.org/10.3389/fphar.2018.00923] [PMID: 30186166]
[17]
Okimoto, N.; Futatsugi, N.; Fuji, H.; Suenaga, A.; Morimoto, G.; Yanai, R.; Ohno, Y.; Narumi, T.; Taiji, M. High-performance drug dis-covery: computational screening by combining docking and molecular dynamics simulations. PLOS Comput. Biol., 2009, 5(10), e1000528.
[http://dx.doi.org/10.1371/journal.pcbi.1000528] [PMID: 19816553]
[18]
Han, Y.; Zhang, J.; Hu, C.Q.; Zhang, X.; Ma, B.; Zhang, P. in silico ADME and toxicity prediction of ceftazidime and its impurities. Front. Pharmacol., 2019, 10, 434.
[http://dx.doi.org/10.3389/fphar.2019.00434] [PMID: 31068821]
[19]
Zhu, J.; Wu, Y.; Xu, L.; Jin, J. Theoretical studies on the selectivity mechanisms of Glycogen Synthase Kinase 3β (GSK3β) with Pyrazine ATP-competitive inhibitors by 3DQSAR, molecular docking, molecular dynamics simulation and free energy calculations. Curr. Computeraided Drug Des., 2020, 16(1), 17-30.
[http://dx.doi.org/10.2174/1573409915666190708102459] [PMID: 31284868]
[20]
Mou, L.; Ma, Z.; Meng, X.; Li, W.; Liang, S.; Chen, X. Exploration of the selective binding mechanism of GSK3β via molecular modeling and molecular dynamics simulation studies. Med. Chem. Res., 2020, 29, 690-698.
[http://dx.doi.org/10.1007/s00044-020-02514-7]
[21]
Jiang, X.; Wang, Y.; Liu, C.; Xing, C.; Wang, Y.; Lyu, W.; Wang, S.; Li, Q.; Chen, T.; Chen, Y.; Feng, F.; Liu, W.; Sun, H. Discovery of potent glycogen synthase kinase 3/cholinesterase inhibitors with neuroprotection as potential therapeutic agent for Alzheimer’s disease. Bioorg. Med. Chem., 2021, 30, 115940.
[http://dx.doi.org/10.1016/j.bmc.2020.115940] [PMID: 33340937]
[22]
El Kerdawy, A.M.; Osman, A.A.; Zaater, M.A. Receptor-based pharmacophore modeling, virtual screening, and molecular docking studies for the discovery of novel GSK-3β inhibitors. J. Mol. Model., 2019, 25(6), 171.
[http://dx.doi.org/10.1007/s00894-019-4032-5] [PMID: 31129879]
[23]
Iwaloye, O.; Elekofehinti, O.O.; Oluwarotimi, E.A.; Kikiowo, B.I.; Fadipe, T.M. Insight into glycogen synthase kinase-3β inhibitory activi-ty of phyto-constituents from Melissa officinalis: In silico studies. In Silico Pharmacol., 2020, 8(1), 2.
[http://dx.doi.org/10.1007/s40203-020-00054-x] [PMID: 32968615]
[24]
Jabir, N.R.; Shakil, S.; Tabrez, S.; Khan, M.S.; Rehman, M.T.; Ahmed, B.A. In silico screening of glycogen synthase kinase-3β targeted ligands against acetylcholinesterase and its probable relevance to Alzheimer’s disease. J. Biomol. Struct. Dyn., 2021, 39(14), 5083-5092.
[http://dx.doi.org/10.1080/07391102.2020.1784796] [PMID: 32588759]
[25]
Yalcin, G.; Yildiz, I. Molecular binding profile of protoberberine alkaloids on glycogen synthase kinase 3β as a drug candidate for Alz-heimer’s diseases. Ankara Univ Eczac Fak Derg., 2018, 42, 1-12.
[26]
Chen, X.; Liu, M.; Gilson, M.K.; Binding, D.B. A web-accessible molecular recognition database. Comb. Chem. High Throughput Screen., 2001, 4(8), 719-725.
[http://dx.doi.org/10.2174/1386207013330670] [PMID: 11812264]
[27]
Discovery Studio 3.5 Client; Accelrys Software Inc, 2012.
[28]
Venkatachalam, C.M.; Jiang, X.; Oldfield, T.; Waldman, M. LigandFit: A novel method for the shape-directed rapid docking of ligands to protein active sites. J. Mol. Graph. Model., 2003, 21(4), 289-307.
[http://dx.doi.org/10.1016/S1093-3263(02)00164-X] [PMID: 12479928]
[29]
Case, D.A.; Babin, V.; Berryman, J.T.; Betz, R.M.; Cai, Q.; Cerutti, D.S. Cheatham, IIITE; Darden, TA; Duke, RE; Gohlke, H; Goetz, AW; Gusarov, S.; Homeyer, N.; Janowski, P.; Kaus, J.; I. Kolossváry, AK; Lee, TS; LeGrand, S; Luchko, T; Luo, R; Madej, B; Merz, KM; Paesani, F; Roe, DR; Roitberg, CSA; Salomon-Ferrer, R; Seabra, G; Simmerling, CL; Smith, W; Swails, J; Walker, RC; Wang, J; Wolf X, RM; Kollman, WPA AMBER14; University of California: San Francisco, 2014.
[30]
Cai, Z.; Zhao, Y.; Zhao, B. Roles of glycogen synthase kinase 3 in Alzheimer’s disease. Curr. Alzheimer Res., 2012, 9(7), 864-879.
[http://dx.doi.org/10.2174/156720512802455386] [PMID: 22272620]
[31]
Uemura, K.; Kuzuya, A.; Shimozono, Y.; Aoyagi, N.; Ando, K.; Shimohama, S.; Kinoshita, A. GSK3β activity modifies the localization and function of presenilin 1. J. Biol. Chem., 2007, 282(21), 15823-15832.
[http://dx.doi.org/10.1074/jbc.M610708200] [PMID: 17389597]
[32]
Ly, P.T.T.; Wu, Y.; Zou, H.; Wang, R.; Zhou, W.; Kinoshita, A.; Zhang, M.; Yang, Y.; Cai, F.; Woodgett, J.; Song, W. Inhibition of GSK3β-mediated BACE1 expression reduces Alzheimer-associated phenotypes. J. Clin. Invest., 2013, 123(1), 224-235.
[http://dx.doi.org/10.1172/JCI64516] [PMID: 23202730]
[33]
Gombar, V.K.; Enslein, K.; Blake, B.W. Assessment of developmental toxicity potential of chemicals by quantitative structure-toxicity relationship models. Chemosphere, 1995, 31(1), 2499-2510.
[http://dx.doi.org/10.1016/0045-6535(95)00119-S] [PMID: 7670862]
[34]
Jain, A.K.; Singh, D.; Dubey, K.; Maurya, R.; Mittal, S.; Pandey, A.K. Models and methods for in vitro toxicity. In: in vitro toxicology; Elsevier Inc., 2018, pp. 45-65.
[http://dx.doi.org/10.1016/B978-0-12-804667-8.00003-1]
[35]
Bertrand, J.A.; Thieffine, S.; Vulpetti, A.; Cristiani, C.; Valsasina, B.; Knapp, S.; Kalisz, H.M.; Flocco, M. Structural characterization of the GSK-3beta active site using selective and non-selective ATP-mimetic inhibitors. J. Mol. Biol., 2003, 333(2), 393-407.
[http://dx.doi.org/10.1016/j.jmb.2003.08.031] [PMID: 14529625]
[36]
Mishra, H.; Kesharwani, R.K.; Singh, D.B.; Tripathi, S.; Dubey, S.K.; Misra, K. Computational simulation of inhibitory effects of curcumin, retinoic acid, and their conjugates on GSK-3 beta. Netw. Model. Anal. Health Inform. Bioinform., 2019, 8, 3.
[http://dx.doi.org/10.1007/s13721-018-0177-x]
[37]
Babu, P.A.; Chitti, S.; Rajesh, B.; Prasanth, V.V.; Kishen, J.V.R.; Vali, R.K. In silico based ligand design and docking studies of GSK-3β inhibitors. Chem-Bio Informatics J., 2010, 10(1), 1-12.
[http://dx.doi.org/10.1273/cbij.10.1]
[38]
Saravanan, K.; Hunday, G.; Kumaradhas, P. Binding and stability of indirubin-3-monoxime in the GSK3β enzyme: A molecular dynamics simulation and binding free energy study. J. Biomol. Struct. Dyn., 2020, 38(4), 957-974.
[http://dx.doi.org/10.1080/07391102.2019.1591301] [PMID: 30963817]

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