Prediction of binding affinity of 1,2-diphenyline ketone analogues at adenosine triphosphate binding site of glycogen synthase kinase-3β: a molecular docking and dynamic simulation study

References

• Bertrand, J. A., Thieffine, S., Vulpetti, A., Cristiani, C., Valsasina, B., Knapp, S., Kalisz, H. M., & Flocco, M. (2003). Structural characterization of the GSK-3beta active site using selective and non-selective ATP-mimetic inhibitors . Journal of Molecular Biology, 333(2), 393–407. https://doi.org/10.1016/j.jmb.2003.08.031
   PubMed Web of Science ®Google Scholar
• Bijur, G. N., & Jope, R. S. (2000). Opposing actions of phosphatidylinositol 3-kinase and glycogen synthase kinase-3beta in the regulation of HSF-1 activity. Journal of Neurochemistry, 75(6), 2401–2408. https://doi.org/10.1046/j.1471-4159.2000.0752401.x
   PubMed Web of Science ®Google Scholar
• Bouskila, M., Hunter, R. W., Ibrahim, A. F. M., Delattre, L., Peggie, M., Van Diepen, J. A., Voshol, P. J., Jensen, J., & Sakamoto, K. (2010). Allosteric regulation of glycogen synthase controls glycogen synthesis in muscle. Cell Metabolism, 12(5), 456–466. https://doi.org/10.1016/j.cmet.2010.10.006
   PubMed Web of Science ®Google Scholar
• Cruz, M. I., Cidade, H., & Pinto, M. (2017). Dual/multitargeted xanthone derivatives for Alzheimer’s disease: where do we stand? Future Medicinal Chemistry, 9(14), 1611–1630. https://doi.org/10.4155/FMC-2017-0086
   PubMed Web of Science ®Google Scholar
• Davie, C. A. (2008). A review of Parkinson's disease. British Medical Bulletin, 86(1), 109–127. https://doi.org/10.1093/bmb/ldn013
   PubMed Web of Science ®Google Scholar
• Dawson, W., & Gygi, F. (2018). Equilibration and analysis of first-principles molecular dynamics simulations of water. The Journal of Chemical Physics, 148(12), 124501. https://doi.org/10.1063/1.5018116
   PubMed Web of Science ®Google Scholar
• Dhananjayan, K. (2015). Molecular docking study characterization of rare flavonoids at the Nac-binding site of the first Bromodomain of BRD4 (BRD4 BD1). Journal of Cancer Research, 2015, 1–15. https://doi.org/10.1155/2015/762716
   Google Scholar
• Dias, R., & de Azevedo, W. F. (2008). Molecular docking algorithms. Current Drug Targets, 9(12), 1040–1047. https://doi.org/10.2174/138945008786949432
   PubMed Web of Science ®Google Scholar
• Dominguez, I., Itoh, K., & Sokol, S. Y. (1995). Role of glycogen synthase kinase 3 beta as a negative regulator of dorsoventral axis formation in Xenopus embryos. Proceedings of the National Academy of Sciences of the United States of America, 92(18), 8498–8502. https://doi.org/10.1073/pnas.92.18.8498
   PubMed Web of Science ®Google Scholar
• Duan, C., Li, M., & Rui, L. (2004). SH2-B Promotes Insulin Receptor Substrate 1 (IRS1)- and IRS2-mediated activation of the phosphatidylinositol 3-kinase pathway in response to leptin. The Journal of Biological Chemistry, 279(42), 43684–43691. https://doi.org/10.1074/jbc.M408495200
   PubMed Web of Science ®Google Scholar
• Duffy, E. M., & Jorgensen, W. L. (2000). Prediction of properties from simulations: Free energies of solvation in hexadecane, octanol, and water. Journal of the American Chemical Society, 122(12), 2878–2888. https://doi.org/10.1021/JA993663T/SUPPL_FILE/JA993663T_S.PDF
   Web of Science ®Google Scholar
• Eldar-Finkelman, H., & Martinez, A. (2011). GSK-3 Inhibitors: Preclinical and Clinical Focus on CNS. Frontiers in Molecular Neuroscience, 4, 32. https://doi.org/10.3389/fnmol.2011.00032
   PubMed Web of Science ®Google Scholar
• Fotie, J., & Bohle, D. S. (2006). Pharmacological and biological activities of xanthones. Anti-Infective Agents in Medicinal Chemistry, 5(1), 15–31. https://doi.org/10.2174/187152106774755563
   Google Scholar
• Freyberg, Z., Ferrando, S. J., & Javitch, J. A. (2010). Roles of the Akt/GSK-3 and Wnt signaling pathways in schizophrenia and antipsychotic drug action. The American Journal of Psychiatry, 167(4), 388–396. https://doi.org/10.1176/appi.ajp.2009.08121873
   PubMed Web of Science ®Google Scholar
• Friesner, R. A., Banks, J. L., Murphy, R. B., Halgren, T. A., Klicic, J. J., Mainz, D. T., Repasky, M. P., Knoll, E. H., Shelley, M., Perry, J. K., Shaw, D. E., Francis, P., & Shenkin, P. S. (2004). Glide: a new approach for rapid, accurate docking and scoring. 1. Method and assessment of docking accuracy. Journal of Medicinal Chemistry, 47(7), 1739–1749. https://doi.org/10.1021/JM0306430/SUPPL_FILE/JM0306430_S.PDF
   PubMed Web of Science ®Google Scholar
• Hernandez, F., Lucas, J. J., & Avila, J. (2013). GSK3 and tau: two convergence points in Alzheimer’s disease. Journal of Alzheimer’s Disease, 33(SUPPL. 1):S141–S144. https://doi.org/10.3233/JAD-2012-129025
   Google Scholar
• Jorgensen, W. L., & Duffy, E. M. (2000). Prediction of drug solubility from Monte Carlo simulations. Bioorganic & Medicinal Chemistry Letters, 10(11), 1155–1158. https://doi.org/10.1016/S0960-894X(00)00172-4
   PubMed Web of Science ®Google Scholar
• Jorgensen, W. L., & Duffy, E. M. (2002). Prediction of drug solubility from structure. Advanced Drug Delivery Reviews, 54(3), 355–366. https://doi.org/10.1016/S0169-409X(02)00008-X
   PubMed Web of Science ®Google Scholar
• Kalinderi, K., Fidani, L., Katsarou, Z., Clarimón, J., Bostantjopoulou, S., & Kotsis, A. (2011). GSK3β polymorphisms, MAPT H1 haplotype and Parkinson's disease in a Greek cohort. Neurobiology of Aging, 32(3), 546.e1–546.e5. https://doi.org/10.1016/j.neurobiolaging.2009.05.007
   PubMed Web of Science ®Google Scholar
• Kapla, J., Espigares, I. R., Ballante, F., Selent, J., & Carlsson, J. (2021). Can molecular dynamics simulations improve the structural accuracy and virtual screening performance of GPCR models? PLoS Computational Biology, 17(5), e1008936. https://doi.org/10.1371/journal.pcbi.1008936
   PubMed Web of Science ®Google Scholar
• Kim, W. Y., Zhou, F. Q., Zhou, J., Yokota, Y., Wang, Y. M., Yoshimura, T., Kaibuchi, K., Woodgett, J. R. R., Anton, E. S., & Snider, W. D. D. (2006). Essential roles for GSK-3s and GSK-3-primed substrates in neurotrophin-induced and hippocampal axon growth. Neuron, 52(6), 981–996. https://doi.org/10.1016/j.neuron.2006.10.031
   PubMed Web of Science ®Google Scholar
• Knapp, B., Frantal, S., Cibena, M., Schreiner, W., & Bauer, P. (2011). Is an intuitive convergence definition of molecular dynamics simulations solely based on the root mean square deviation possible? Journal of Computational Biology, 18(8), 997–1005. https://doi.org/10.1089/cmb.2010.0237
   PubMed Web of Science ®Google Scholar
• Kwok, J. B. J., Hallupp, M., Loy, C. T., Chan, D. K. Y., Woo, J., Mellick, G. D., Buchanan, D. D., Silburn, P. A., Halliday, G. M., & Schofield, P. R. (2005). GSK3B polymorphisms alter transcription and splicing in Parkinson’s disease. Annals of Neurology, 58(6), 829–839. https://doi.org/10.1002/ana.20691
   PubMed Web of Science ®Google Scholar
• Lawrence, J. C., & Roach, P. J. (1997). New insights into the role and mechanism of glycogen synthase activation by insulin. Diabetes, 46(4), 541–547. https://doi.org/10.2337/diab.46.4.541
   PubMed Web of Science ®Google Scholar
• Leng, S., Zhang, W., Zheng, Y., Liberman, Z., Rhodes, C. J., Eldar-Finkelman, H., & Sun, X. J. (2010). Glycogen synthase kinase 3 beta mediates high glucose-induced ubiquitination and proteasome degradation of insulin receptor substrate 1. The Journal of Endocrinology, 206(2), 171–181. https://doi.org/10.1677/JOE-09-0456
   PubMed Web of Science ®Google Scholar
• Lipinski, C. A. (2004). Lead- and drug-like compounds: the rule-of-five revolution. Drug Discovery Today. Technologies, 1(4), 337–341. https://doi.org/10.1016/j.ddtec.2004.11.007
   PubMedGoogle Scholar
• Lipinski, C. A., Lombardo, F., Dominy, B. W., & Feeney, P. J. (1997). Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Advanced Drug Delivery Reviews, 23(1-3), 3–25. https://doi.org/10.1016/S0169-409X(96)00423-1
   Web of Science ®Google Scholar
• Lu, S. Y., Huang, Z-M., Huang, W-K., Liu, X-Y., Chen, Y-Y., Shi, T., & Zhang, J. (2013). How calcium inhibits the magnesium-dependent kinase gsk3β: a molecular simulation study. Proteins, 81(5), 740–753. https://doi.org/10.1002/PROT.24221
   PubMed Web of Science ®Google Scholar
• Lu, S. Y., Jiang, Y. J., Lv, J., Zou, J. W., & Wu, T. X. (2011). Role of bridging water molecules in GSK3β-inhibitor complexes: Insights from QM/MM, MD, and molecular docking studies. Journal of Computational Chemistry, 32(9), 1907–1918. https://doi.org/10.1002/jcc.21775
   PubMed Web of Science ®Google Scholar
• Luo, J. (2012). The role of GSK3beta in the development of the central nervous system. Frontiers in Biology, 7(3), 212–220. https://doi.org/10.1007/s11515-012-1222-2
   Google Scholar
• Madhavi Sastry, G., Adzhigirey, M., Day, T., Annabhimoju, R., & Sherman, W. (2013). Protein and ligand preparation: parameters, protocols, and influence on virtual screening enrichments. Journal of Computer-Aided Molecular Design, 27(3), 221–234. https://doi.org/10.1007/s10822-013-9644-8
   PubMed Web of Science ®Google Scholar
• Martin, L., Magnaudeix, A., Esclaire, F., Yardin, C., & Terro, F. (2009). Inhibition of glycogen synthase kinase-3beta downregulates total tau proteins in cultured neurons and its reversal by the blockade of protein phosphatase-2A. Brain Research, 1252, 66–75. https://doi.org/10.1016/j.brainres.2008.11.057
   PubMed Web of Science ®Google Scholar
• Martin, M., Rehani, K., Jope, R. S., & Michalek, S. M. (2005). Toll-like receptor-mediated cytokine production is differentially regulated by glycogen synthase kinase 3. Nature Immunology, 6(8), 777–784. https://doi.org/10.1038/ni1221
   PubMed Web of Science ®Google Scholar
• Ntie-Kang, F. (2013). An in silico evaluation of the ADMET profile of the StreptomeDB database. SpringerPlus, 2(1), 353–311. https://doi.org/10.1186/2193-1801-2-353
   PubMedGoogle Scholar
• Ntie-Kang, F., Lifongo, L. L., Mbah, J. A., Owono, L. C., Megnassan, E., Mbaze, L. M., Judson, P. N., Sippl, W., & Efange, S. M. N. (2013). In silico drug metabolism and pharmacokinetic profiles of natural products from medicinal plants in the Congo basin. In Silico Pharmacology, 1(1), 12. https://doi.org/10.1186/2193-9616-1-12
   PubMedGoogle Scholar
• Pace, N. J., & Weerapana, E. (2014). Zinc-binding cysteines: diverse functions and structural motifs. Biomolecules, 4(2), 419–434. https://doi.org/10.3390/BIOM4020419
   PubMedGoogle Scholar
• Pei, J. J., Braak, E., Braak, H., Grundke-Iqbal, I., Iqbal, K., Winblad, B., & Cowburn, R. F. (1999). Distribution of active glycogen synthase kinase 3beta (GSK-3beta) in brains staged for Alzheimer disease neurofibrillary changes. Journal of Neuropathology and Experimental Neurology, 58(9), 1010–1019. https://doi.org/10.1097/00005072-199909000-00011
   PubMed Web of Science ®Google Scholar
• Pinto, M. M. M., Castanheiro, R. A. P., & Kijjoa, A. (2014). Xanthones from marine-derived microorganisms: isolation, structure elucidation and biological activities. In R.A. Meyers (Ed.), Encyclopedia of analytical chemistry (pp. 1–21). London, UK: John Wiley & Sons, Inc. https://doi.org/10.1002/9780470027318.A9927
   Google Scholar
• Piras, R., Rothman, L. B., & Cabib, E. (1968). Regulation of muscle glycogen synthetase by metabolites. Differential effects on the I and D forms. Biochemistry, 7(1), 56–66. https://doi.org/10.1021/bi00841a009
   PubMed Web of Science ®Google Scholar
• Rodionova, E., Conzelmann, M., Maraskovsky, E., Hess, M., Kirsch, M., Giese, T., Ho, A. D., Zöller, M., Dreger, P., & Luft, T. (2007). GSK-3 mediates differentiation and activation of proinflammatory dendritic cells. Blood, 109(4), 1584–1592. https://doi.org/10.1182/blood-2006-06-028951
   PubMed Web of Science ®Google Scholar
• Salahudeen, M. S., & Nishtala, P. S. (2017). An overview of pharmacodynamic modelling, ligand-binding approach and its application in clinical practice. Saudi Pharmaceutical Journal, 25(2), 165–175. https://doi.org/10.1016/j.jsps.2016.07.002
   PubMed Web of Science ®Google Scholar
• Sander, T., Freyss, J., Von Korff, M., & Rufener, C. (2015). DataWarrior: an open-source program for chemistry aware data visualization and analysis. Journal of Chemical Information and Modeling, 55(2), 460–473. https://doi.org/10.1021/ci500588j
   PubMed Web of Science ®Google Scholar
• Sargsyan, K., Grauffel, C., & Lim, C. (2017). How molecular size impacts RMSD applications in molecular dynamics simulations. Journal of Chemical Theory and Computation, 13(4), 1518–1524. https://doi.org/10.1021/ACS.JCTC.7B00028/SUPPL_FILE/CT7B00028_SI_001.PDF
   PubMed Web of Science ®Google Scholar
• Schrödinger Release 2021-4. (2021a). Desmond | Schrödinger. D. E. Shaw Research. https://www.schrodinger.com/products/desmond
   Google Scholar
• Schrödinger Release 2021-4 (2021b). Glide | Schrödinger. https://www.schrodinger.com/products/glide
   Google Scholar
• Shahid, S., Jamal, Q., Arif, J., Al-Khodairy, F., Dhasmana, A., & Lohani, M. (2015). In silico molecular docking analysis to predict the role of metal ions in the function of drug targeted proteins. World Journal of Pharmaceutical Research, 4, 132–144. https://scholarworks.utrgv.edu/som_pub/173
   Google Scholar
• Shelley, J. C., Cholleti, A., Frye, L. L., Greenwood, J. R., Timlin, M. R., & Uchimaya, M. (2007). Epik: a software program for pKa prediction and protonation state generation for drug-like molecules. Journal of Computer-Aided Molecular Design, 21(12), 681–691. https://doi.org/10.1007/S10822-007-9133-Z/TABLES/5
   PubMed Web of Science ®Google Scholar
• Solomon, E. I., Heppner, D. H., Johnston, E. M., Ginsbach, J. W., Cirera, J., Qayyum, M., Kieber-Emmons, M.T., Kjaergaard, C. H., Hadt, R. G., & Tian, L. (2014). Copper active sites in biology. Chemical Reviews, 114(7), 3659–3853. https://doi.org/10.1021/CR400327T
   PubMed Web of Science ®Google Scholar
• Tchamo Diderot, N., Silvere, N., & Etienne, T. (2006). Xanthones as therapeutic agents: chemistry and pharmacology. Advances in Phytomedicine, 2(C), 273–298. https://doi.org/10.1016/S1572-557X(05)02016-7
   Google Scholar
• Trivedi, N., Marsh, P., Goold, R. G., Wood-Kaczmar, A., & Gordon-Weeks, P. R. (2005). Glycogen synthase kinase-3beta phosphorylation of MAP1B at Ser1260 and Thr1265 is spatially restricted to growing axons. Journal of Cell Science, 118(Pt 5), 993–1005. https://doi.org/10.1242/jcs.01697
   PubMed Web of Science ®Google Scholar
• Walz, A., Ugolkov, A., Chandra, S., Kozikowski, A., Carneiro, B. A., O'Halloran, T. V., Giles, F. J., Billadeau, D. D., & Mazar, A. P. (2017). Molecular pathways: revisiting glycogen synthase kinase-3β as a target for the treatment of cancer. Clinical Cancer Research, 23(8), 1891–1897. https://doi.org/10.1158/1078-0432.CCR-15-2240
   PubMed Web of Science ®Google Scholar
• Woodgett, J. R. (1991). cDNA cloning and properties of glycogen synthase kinase-3. Methods in Enzymology, 200(C), 564–577. https://doi.org/10.1016/0076-6879(91)00172-S
   PubMedGoogle Scholar
• Wu, D., & Pan, W. (2010). GSK3: a multifaceted kinase in Wnt signaling. Trends in Biochemical Sciences, 35(3), 161–168. https://doi.org/10.1016/j.tibs.2009.10.002
   PubMed Web of Science ®Google Scholar
• Zhang, Y., Huang, N-Q., Yan, F., Jin, H., Zhou, S., Yu, S. J., Shan., & Jin, F. (2018). Diabetes mellitus and Alzheimer's disease: GSK-3β as a potential link. Behavioural Brain Research, 339, 57–65. https://doi.org/10.1016/j.bbr.2017.11.015
   PubMed Web of Science ®Google Scholar
• Zheng, H., Cooper, D. R., Porebski, P. J., Shabalin, I. G., Handing, K. B., & Minor, W. (2017). CheckMyMetal: a macromolecular metal-binding validation tool. Acta Crystallographica. Section D, Structural Biology, 73(Pt 3), 223–233. https://doi.org/10.1107/S2059798317001061
   PubMedGoogle Scholar