Identifying potential Alzheimer's disease therapeutics through GSK-3β inhibition: : A molecular docking and dynamics approach
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Yasaman Mohammadi, Reza Emadi, Arman Maddahi, Shiva Shirdel, Mohammad Hossein MorowvatAuthors Info & Claims
Yasaman Mohammadi, Reza Emadi, Arman Maddahi, Shiva Shirdel, Mohammad Hossein MorowvatAuthors Info & ClaimsGraphical Abstract
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[1]
I. Akbarzadeh, A. Saremi Poor, M. Khodarahmi, M. Abdihaji, A. Moammeri, S. Jafari, et al., Gingerol/letrozole-loaded mesoporous silica nanoparticles for breast cancer therapy: In-silico and in-vitro studies, Microporous Mesoporous Mater. 337 (2022).
[2]
R. Bhat, Y. Xue, S. Berg, S. Hellberg, M. Ormö, Y. Nilsson, et al., Structural insights and biological effects of glycogen synthase kinase 3-specific inhibitor AR-A014418, J. Biol. Chem. 278 (46) (2003) 45937–45945.
[3]
A.P. Bhati, S. Wan, D.W. Wright, P.V. Coveney, Rapid, accurate, precise, and reliable relative free energy prediction using ensemble based thermodynamic integration, J. Chem. Theory Comput. 13 (1) (2017) 210–222.
[4]
Z. Breijyeh, R. Karaman, Comprehensive review on Alzheimer's disease: causes and treatment, Molecules 25 (24) (2020).
[5]
R. Buonfiglio, F. Prati, M. Bischetti, C. Cavarischia, G. Furlotti, R. Ombrato, Discovery of novel imidazopyridine GSK-3β inhibitors supported by computational approaches, Molecules 25 (9) (2020) 2163.
[6]
D.A. Case, H.M. Aktulga, K. Belfon, D.S. Cerutti, G.A. Cisneros, V.W.D. Cruzeiro, et al., AmberTools, J. Chem. Inf. Model. (2023).
[7]
P. Cohen, Protein kinases—the major drug targets of the twenty-first century?, Nat. Rev. Drug Discov. 1 (4) (2002) 309–315.
[8]
P.V. Coveney, S. Wan, On the calculation of equilibrium thermodynamic properties from molecular dynamics, Phys. Chem. Chem. Phys. 18 (44) (2016) 30236–30240.
[9]
J. Cummings, G. Lee, A. Ritter, M. Sabbagh, K. Zhong, Alzheimer's disease drug development pipeline: 2019, Alzheimer'S. Dement.: Transl. Res. Clin. Interv. 5 (2019) 272–293.
[10]
P. Czeleń, Molecular dynamics study on inhibition mechanism of CDK-2 and GSK-3β by CHEMBL272026 molecule, Struct. Chem. 27 (2016) 1807–1818.
[11]
U. Essmann, L. Perera, M.L. Berkowitz, T. Darden, H. Lee, L.G. Pedersen, A smooth particle mesh Ewald method, J. Chem. Phys. 103 (19) (1995) 8577–8593.
[12]
B. Farasati Far, S. Asadi, M.R. Naimi-Jamal, W.K. Abdelbasset, A. Aghajani Shahrivar, Insights into the interaction of azinphos-methyl with bovine serum albumin: experimental and molecular docking studies, J. Biomol. Struct. Dyn. 40 (22) (2022) 11863–11873.
[13]
B. Farasati Far, D. Bokov, G. Widjaja, H. Setia Budi, W. Kamal Abdelbasset, S. Javanshir, et al., Metronidazole, acyclovir and tetrahydrobiopterin may be promising to treat COVID-19 patients, through interaction with interleukin-12, J. Biomol. Struct. Dyn. 41 (10) (2023) 4253–4271.
[14]
F. Hernández, E.G. de Barreda, A. Fuster-Matanzo, J.J. Lucas, J. Avila, GSK3: a possible link between beta amyloid peptide and tau protein, Exp. Neurol. 223 (2) (2010) 322–325.
[15]
B. Hess, H. Bekker, H.J. Berendsen, J.G. Fraaije, LINCS: a linear constraint solver for molecular simulations, J. Comput. Chem. 18 (12) (1997) 1463–1472.
[16]
B. Honarvari, S. Karimifard, N. Akhtari, M. Mehrarya, Z.S. Moghaddam, M.J. Ansari, et al., Folate-targeted curcumin-loaded niosomes for site-specific delivery in breast cancer treatment: In Silico and In Vitro study, Molecules 27 (14) (2022) 4634.
[17]
M. Khaleghian, H. Sahrayi, Y. Hafezi, M. Mirshafeeyan, Z.S. Moghaddam, B. Farasati Far, et al., In silico design and mechanistic study of niosome-encapsulated curcumin against multidrug-resistant Staphylococcus aureus biofilms, Front Microbiol 14 (2023) 1277533.
[18]
P. Khanal, F. Zargari, B.F. Far, D. Kumar, Y.K. Mahdi, N.K. Jubair, et al., Integration of system biology tools to investigate huperzine A as an anti-Alzheimer agent, Front Pharm. 12 (2021).
[19]
M.A. Khanfar, R.A. Hill, A. Kaddoumi, K.A. El Sayed, Discovery of novel GSK-3β inhibitors with potent in vitro and in vivo activities and excellent brain permeability using combined ligand-and structure-based virtual screening, J. Med. Chem. 53 (24) (2010) 8534–8545.
[20]
B. Knapp, L. Ospina, C.M. Deane, Avoiding false positive conclusions in molecular simulation: the importance of replicas, J. Chem. Theory Comput. 14 (12) (2018) 6127–6138.
[21]
A. Kumar, G. Srivastava, A.S. Negi, A. Sharma, Docking, molecular dynamics, binding energy-MM-PBSA studies of naphthofuran derivatives to identify potential dual inhibitors against BACE-1 and GSK-3β, J. Biomol. Struct. Dyn. 37 (2) (2019) 275–290.
[22]
P. Manoharan, N. Ghoshal, Fragment-based virtual screening approach and molecular dynamics simulation studies for identification of BACE1 inhibitor leads, J. Biomol. Struct. Dyn. 36 (7) (2018) 1878–1892.
[23]
M. Maqbool, M. Mobashir, N. Hoda, Pivotal role of glycogen synthase kinase-3: a therapeutic target for Alzheimer's disease, Eur. J. Med. Chem. 107 (2016) 63–81.
[24]
V. Montagnani, B. Stecca, Role of protein kinases in hedgehog pathway control and implications for cancer therapy, Cancers 11 (4) (2019) 449.
[25]
R.D. Paris, C.V. Quevedo, D.D. Ruiz, Souza ONd, Barros RC. Clustering molecular dynamics trajectories for optimizing docking experiments, Comput. Intell. Neurosci. 2015 (2015) 32.
[26]
S.K. Sadiq, D. Wright, S.J. Watson, S.J. Zasada, I. Stoica, P.V. Coveney, Automated molecular simulation based binding affinity calculator for ligand-bound HIV-1 proteases, ACS Publications, 2008.
[27]
H. Sahrayi, E. Hosseini, A. Ramazani Saadatabadi, S.M. Atyabi, H. Bakhshandeh, M. Mohamadali, et al., Cold atmospheric plasma modification and electrical conductivity induction in gelatin/polyvinylidene fluoride nanofibers for neural tissue engineering, Artif. Organs 46 (8) (2022) 1504–1521.
[28]
A.P. Saraswati, S.A. Hussaini, N.H. Krishna, B.N. Babu, A. Kamal, Glycogen synthase kinase-3 and its inhibitors: potential target for various therapeutic conditions, Eur. J. Med. Chem. 144 (2018) 843–858.
[29]
S. Sargazi, S. Shahraki, O. Shahraki, F. Zargari, R. Sheervalilou, S. Maghsoudi, et al., 8-Alkylmercaptocaffeine derivatives: antioxidant, molecular docking, and in-vitro cytotoxicity studies, Bioorg. Chem. 111 (2021).
[30]
P. Tellechea, N. Pujol, P. Esteve-Belloch, B. Echeveste, M. García-Eulate, J. Arbizu, M. Riverol, Early-and late-onset Alzheimer disease: are they the same entity?, Neurol. ía (Engl. Ed. ) 33 (4) (2018) 244–253.
[31]
E. Ter Haar, J.T. Coll, D.A. Austen, H.-M. Hsiao, L. Swenson, J. Jain, Structure of GSK3β reveals a primed phosphorylation mechanism, Nat. Struct. Biol. 8 (7) (2001) 593–596.
[32]
A.J. Valvezan, P.S. Klein, GSK-3 and Wnt signaling in neurogenesis and bipolar disorder, Front. Mol. Neurosci. 5 (2012) 1.
[33]
S. Wan, R.C. Sinclair, P.V. Coveney, Uncertainty quantification in classical molecular dynamics, Philos. Trans. R. Soc. A 379 (2197) (2021) 20200082.
[34]
Z. Wang, H. Sun, X. Yao, D. Li, L. Xu, Y. Li, et al., Comprehensive evaluation of ten docking programs on a diverse set of protein–ligand complexes: the prediction accuracy of sampling power and scoring power, Phys. Chem. Chem. Phys. 18 (18) (2016) 12964–12975.
[35]
S. Zare, L. Emami, Z. Faghih, F. Zargari, Z. Faghih, S. Khabnadideh, Design, synthesis, computational study and cytotoxic evaluation of some new quinazoline derivatives containing pyrimidine moiety, Sci. Rep. 13 (1) (2023) 14461.
[36]
F. Zargari, Z. Nikfarjam, E. Nakhaei, M. Ghorbanipour, A. Nowroozi, A. Amiri, Study of tyramine-binding mechanism and insecticidal activity of oil extracted from Eucalyptus against Sitophilus oryzae, Front. Chem. 10 (2022).
[37]
D. Zhang, L. Liu, L. Pang, Q. Jin, K. Ke, M. Hu, et al., Biological evaluation and energetic analyses of novel GSK-3β inhibitors, J. Cell. Biochem. 119 (4) (2018) 3510–3518.
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Elsevier Science Publishers B. V.
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Published: 01 August 2024
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