Epigenetic regulation exerted by Caliphruria subedentata and galantamine: an in vitro and in silico approach for mimic Alzheimer’s disease

References

• Adwan, L., & Zawia, N. H. (2013). Epigenetics: A novel therapeutic approach for the treatment of Alzheimer’s disease. Pharmacology & Therapeutics, 139(1), 41–50. https://doi.org/10.1016/j.pharmthera.2013.03.010
   PubMed Web of Science ®Google Scholar
• An, J., Chen, B., Wang, A., Hao, D., Zhang, Q., Zhao, J., Liu, C., Zhang, L., Zhang, R., & Yang, H. (2018). Modulatory effects of natural products on neuronal differentiation.
   Google Scholar
• Aristizabal-Pachon, A. F., & Castillo, W. O. (2017). Role of GSK3β in breast cancer susceptibility. Cancer Biomarkers: Section A of Disease Markers, 18(2), 169–175. https://doi.org/10.3233/CBM-160120
   PubMed Web of Science ®Google Scholar
• Babenko, O., Kovalchuk, I., & Metz, G. A. (2012). Epigenetic programming of neurodegenerative diseases by an adverse environment. Brain Research, 1444, 96–111. https://doi.org/10.1016/j.brainres.2012.01.038
   PubMed Web of Science ®Google Scholar
• Barrachina, M., & Ferrer, I. (2009). DNA methylation of Alzheimer disease and tauopathy-related genes in postmortem brain. Journal of Neuropathology and Experimental Neurology, 68(8), 880–891. https://doi.org/10.1097/NEN.0b013e3181af2e46
   PubMed Web of Science ®Google Scholar
• Beaver, M., Bhatnagar, A., Panikker, P., Zhang, H., Snook, R., Parmar, V., Vijayakumar, G., Betini, N., Akhter, S., & Elefant, F. (2020). Disruption of Tip60 HAT mediated neural histone acetylation homeostasis is an early common event in neurodegenerative diseases. Scientific Reports, 10(1), 18265. https://doi.org/10.1038/s41598-020-75035-3
   PubMed Web of Science ®Google Scholar
• Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, N., & Bourne, P. E. (2000). The protein data bank. Nucleic Acids Research, 28(1), 235–242. https://doi.org/10.1093/nar/28.1.235
   PubMed Web of Science ®Google Scholar
• Cabezas, F., Pigni, N., Bastida, J., Codina, C., & Viladomat, F. (2013). Análisis del contenido alcaloidico de Caliphruria Subdentata Baker (Amaryllidaceae) por el método CG-EM. Revista Latinoamericana de Química, 41(1), 68–73.
   Google Scholar
• Castillo-Ordóñez, W. O., Tamarozzi, E. R., da Silva, G. M., Aristizabal-Pachón, A. F., Sakamoto-Hojo, E. T., Takahashi, C. S., & Giuliatti, S. (2017). Exploration of the acetylcholinesterase inhibitory activity of some alkaloids from amaryllidaceae family by molecular docking in silico. Neurochemical Research, 42(10), 2826–2830. https://doi.org/10.1007/s11064-017-2295-8
   PubMed Web of Science ®Google Scholar
• Castillo, W. O., Aristizabal-Pachon, A. F., de Lima Montaldi, A. P., Sakamoto-Hojo, E. T., & Takahashi, C. S. (2016). Galanthamine decreases genotoxicity and cell death induced by β-amyloid peptide in SH-SY5Y cell line. Neurotoxicology, 57, 291–297. https://doi.org/10.1016/j.neuro.2016.10.013
   PubMed Web of Science ®Google Scholar
• Castillo, W. O., Aristizabal-Pachon, A. F., Sakamoto-Hojo, E., Gasca, C. A., Cabezas-Fajardo, F. A., & Takahashi, C. (2018). Caliphruria subedentata (Amaryllidaceae) decreases genotoxicity and cell death induced by β-amyloid peptide in sh-sy5y cell line. Mutation Research. Genetic Toxicology and Environmental Mutagenesis, 836(Pt B), 54–61. https://doi.org/10.1016/j.mrgentox.2018.06.010
   PubMedGoogle Scholar
• Chen, J., & Shen, B. (2009). Computational analysis of amino acid mutation: A proteome wide perspective. Current Proteomics, 6(4), 228–234. https://doi.org/10.2174/157016409789973734
   Web of Science ®Google Scholar
• Chen, L., Guo, X., Li, Z., & He, Y. (2019). Relationship between long non-coding RNAs and Alzheimer’s disease: A systematic review. Pathology, Research and Practice, 215(1), 12–20. https://doi.org/10.1016/j.prp.2018.11.012
   PubMed Web of Science ®Google Scholar
• Coccini, T., Manzo, L., Bellotti, V., & De Simone, U. (2014). Assessment of cellular responses after short-and long-term exposure to silver nanoparticles in human neuroblastoma (SH-SY5Y) and astrocytoma (D384) cells. The Scientific World Journal, 2014, 1–13. https://doi.org/10.1155/2014/259765
   Google Scholar
• Cortes, N., Castañeda, C., Osorio, E. H., Cardona-Gomez, G. P., & Osorio, E. (2018). Amaryllidaceae alkaloids as agents with protective effects against oxidative neural cell injury. Life Sciences, 203, 54–65. https://doi.org/10.1016/j.lfs.2018.04.026
   PubMed Web of Science ®Google Scholar
• de Medeiros, L. M., De Bastiani, M. A., Rico, E. P., Schonhofen, P., Pfaffenseller, B., Wollenhaupt-Aguiar, B., Grun, L., Barbé-Tuana, F., Zimmer, E. R., Castro, M. A. A., Parsons, R. B., & Klamt, F. (2019). Cholinergic differentiation of human neuroblastoma SH-SY5Y cell line and its potential use as an in vitro model for Alzheimer’s disease studies. Molecular Neurobiology, 56(11), 7355–7367. https://doi.org/10.1007/s12035-019-1605-3
   PubMed Web of Science ®Google Scholar
• Ezoulin, M. J. M., Ombetta, J.-E., Dutertre-Catella, H., Warnet, J.-M., & Massicot, F. (2008). Antioxidative properties of galantamine on neuronal damage induced by hydrogen peroxide in SK–N–SH cells. Neurotoxicology, 29(2), 270–277. https://doi.org/10.1016/j.neuro.2007.11.004
   PubMed Web of Science ®Google Scholar
• Felsenstein, K. M., Candelario, K. M., Steindler, D. A., & Borchelt, D. R. (2014). Regenerative medicine in Alzheimer’s disease. Translational Research : The Journal of Laboratory and Clinical Medicine, 163(4), 432–438. https://doi.org/10.1016/j.trsl.2013.11.001
   PubMed Web of Science ®Google Scholar
• Fuso, A., Cavallaro, R. A., Zampelli, A., D'Anselmi, F., Piscopo, P., Confaloni, A., & Scarpa, S. (2007). γ-Secretase is differentially modulated by alterations of homocysteine cycle in neuroblastoma and glioblastoma cells. Journal of Alzheimer’s Disease, 11(3), 275–290. https://doi.org/10.3233/jad-2007-11303
   PubMed Web of Science ®Google Scholar
• Fuso, A., Nicolia, V., Pasqualato, A., Fiorenza, M. T., Cavallaro, R. A., & Scarpa, S. (2011). Changes in Presenilin 1 gene methylation pattern in diet-induced B vitamin deficiency. Neurobiology of Aging, 32(2), 187–199. https://doi.org/10.1016/j.neurobiolaging.2009.02.013
   PubMed Web of Science ®Google Scholar
• Ganai, S. A., Abdullah, E., Rashid, R., & Altaf, M. (2017). Combinatorial in silico strategy towards identifying potential hotspots during inhibition of structurally identical HDAC1 and HDAC2 enzymes for effective chemotherapy against neurological disorders. Frontiers in Molecular Neuroscience, 10, 357. https://doi.org/10.3389/fnmol.2017.00357
   PubMed Web of Science ®Google Scholar
• Gangisetty, O., & Murugan, S. (2016). Epigenetic modifications in neurological diseases: Natural products as epigenetic modulators a treatment strategy, The benefits of natural products for neurodegenerative diseases (pp. 1–25). Springer.
   Google Scholar
• Guan, J.-S., Haggarty, S. J., Giacometti, E., Dannenberg, J.-H., Joseph, N., Gao, J., Nieland, T. J. F., Zhou, Y., Wang, X., Mazitschek, R., Bradner, J. E., DePinho, R. A., Jaenisch, R., & Tsai, L.-H. (2009). HDAC2 negatively regulates memory formation and synaptic plasticity. Nature, 459(7243), 55–60. https://doi.org/10.1038/nature07925
   PubMed Web of Science ®Google Scholar
• Hanwell, M. D., Curtis, D. E., Lonie, D. C., Vandermeersch, T., Zurek, E., & Hutchison, G. R. (2012). Avogadro: An advanced semantic chemical editor, visualization, and analysis platform. Journal of Cheminformatics, 4(1), 17. https://doi.org/10.1186/1758-2946-4-17
   PubMed Web of Science ®Google Scholar
• Heinrich, M., & Lee Teoh, H. (2004). Galanthamine from snowdrop—The development of a modern drug against Alzheimer’s disease from local Caucasian knowledge. Journal of Ethnopharmacology, 92(2-3), 147–162. https://doi.org/10.1016/j.jep.2004.02.012
   PubMed Web of Science ®Google Scholar
• Hernandez-Valladares, M., Wangen, R., Berven, F. S., & Guldbrandsen, A. (2019). Protein post-translational modification crosstalk in acute myeloid leukemia calls for action. Current Medicinal Chemistry, 26(28), 5317–5337. https://doi.org/10.2174/0929867326666190503164004
   PubMed Web of Science ®Google Scholar
• Huang, J., Rauscher, S., Nawrocki, G., Ran, T., Feig, M., De Groot, B. L., Grubmüller, H., & MacKerell, A. D. (2017). CHARMM36m: An improved force field for folded and intrinsically disordered proteins. Nature Methods, 14(1), 71–73. https://doi.org/10.1038/nmeth.4067
   PubMed Web of Science ®Google Scholar
• Iraola‐Guzmán, S., Estivill, X., & Rabionet, R. (2011). DNA methylation in neurodegenerative disorders: A missing link between genome and environment? Clinical Genetics, 80(1), 1–14. https://doi.org/10.1111/j.1399-0004.2011.01673.x
   PubMed Web of Science ®Google Scholar
• Jagirdar, R., Drexel, M., Bukovac, A., Tasan, R. O., & Sperk, G. (2016). Expression of class II histone deacetylases in two mouse models of temporal lobe epilepsy. Journal of Neurochemistry, 136(4), 717–730. https://doi.org/10.1111/jnc.13440
   PubMed Web of Science ®Google Scholar
• Janczura, K. J., Volmar, C.-H., Sartor, G. C., Rao, S. J., Ricciardi, N. R., Lambert, G., Brothers, S. P., & Wahlestedt, C. (2018). Inhibition of HDAC3 reverses Alzheimer’s disease-related pathologies in vitro and in the 3xTg-AD mouse model. Proceedings of the National Academy of Sciences of the United States of America, 115(47), E11148–E11157. https://doi.org/10.1073/pnas.1805436115
   PubMed Web of Science ®Google Scholar
• Jin, K., Xie, L., Mao, X. O., & Greenberg, D. A. (2006). Alzheimer’s disease drugs promote neurogenesis. Brain Research, 1085(1), 183–188. https://doi.org/10.1016/j.brainres.2006.02.081
   PubMedGoogle Scholar
• Jones, G., Willett, P., Glen, R. C., Leach, A. R., & Taylor, R. (1997). Development and validation of a genetic algorithm for flexible docking. Journal of Molecular Biology, 267(3), 727–748. https://doi.org/10.1006/jmbi.1996.0897
   PubMed Web of Science ®Google Scholar
• Khan, M. T., Rehaman, A. U., Junaid, M., Malik, S. I., & Wei, D.-Q. (2018). Insight into novel clinical mutants of RpsA-S324F, E325K, and G341R of Mycobacterium tuberculosis associated with pyrazinamide resistance. Computational and Structural Biotechnology Journal, 16, 379–387. https://doi.org/10.1016/j.csbj.2018.09.004
   PubMed Web of Science ®Google Scholar
• Kim, S., Thiessen, P. A., Bolton, E. E., Chen, J., Fu, G., Gindulyte, A., Han, L., He, J., He, S., Shoemaker, B. A., Wang, J., Yu, B., Zhang, J., and Bryant, S. H. (2016). PubChem substance and compound databases. Nucleic Acids Research, 44(D1), D1202–1213. https://doi.org/10.1093/nar/gkv951
   PubMed Web of Science ®Google Scholar
• Kita, Y., Ago, Y., Higashino, K., Asada, K., Takano, E., Takuma, K., & Matsuda, T. (2014). Galantamine promotes adult hippocampal neurogenesis via M1 muscarinic and α7 nicotinic receptors in mice. The International Journal of Neuropsychopharmacology, 17(12), 1957–1968. https://doi.org/10.1017/S1461145714000613
   PubMed Web of Science ®Google Scholar
• Kovalevich, J., & Langford, D. (2013). Considerations for the use of SH-SY5Y neuroblastoma cells in neurobiology, Neuronal cell culture (pp. 9–21). Springer.
   Google Scholar
• Kuehner, J. N., Bruggeman, E. C., Wen, Z., & Yao, B. (2019). Epigenetic regulations in neuropsychiatric disorders. Frontiers in Genetics, 10, 268. https://doi.org/10.3389/fgene.2019.00268
   PubMed Web of Science ®Google Scholar
• Kumari, A., Bhawal, S., Kapila, S., Yadav, H., & Kapila, R. (2022). Health-promoting role of dietary bioactive compounds through epigenetic modulations: A novel prophylactic and therapeutic approach. Critical Reviews in Food Science and Nutrition, 62(3), 619–639. https://doi.org/10.1080/10408398.2020.1825286
   PubMed Web of Science ®Google Scholar
• Kumari, R., Kumar, R., Open Source Drug Discovery Consortium, & Lynn, A. (2014). g_mmpbsa: A GROMACS tool for high-throughput MM-PBSA calculations. Journal of Chemical Information and Modeling, 54(7), 1951–1962. https://doi.org/10.1021/ci500020m
   PubMed Web of Science ®Google Scholar
• Kumbhar, N., Nimal, S., Barale, S., Kamble, S., Bavi, R., Sonawane, K., & Gacche, R. (2022). Identification of novel leads as potent inhibitors of HDAC3 using ligand-based pharmacophore modeling and MD simulation. Scientific Reports, 12(1), 1712. https://doi.org/10.1038/s41598-022-05698-7
   PubMed Web of Science ®Google Scholar
• Lauffer, B. E. L., Mintzer, R., Fong, R., Mukund, S., Tam, C., Zilberleyb, I., Flicke, B., Ritscher, A., Fedorowicz, G., Vallero, R., Ortwine, D. F., Gunzner, J., Modrusan, Z., Neumann, L., Koth, C. M., Lupardus, P. J., Kaminker, J. S., Heise, C. E., & Steiner, P. (2013). Histone deacetylase (HDAC) inhibitor kinetic rate constants correlate with cellular histone acetylation but not transcription and cell viability. The Journal of Biological Chemistry, 288(37), 26926–26943. https://doi.org/10.1074/jbc.M113.490706
   PubMed Web of Science ®Google Scholar
• Linciano, P., Benedetti, R., Pinzi, L., Russo, F., Chianese, U., Sorbi, C., Altucci, L., Rastelli, G., Brasili, L., & Franchini, S. (2021). Investigation of the effect of different linker chemotypes on the inhibition of histone deacetylases (HDACs). Bioorganic Chemistry, 106, 104462. https://doi.org/10.1016/j.bioorg.2020.104462
   PubMed Web of Science ®Google Scholar
• Liu, R., Barkhordarian, H., Emadi, S., Park, C. B., & Sierks, M. R. (2005). Trehalose differentially inhibits aggregation and neurotoxicity of beta-amyloid 40 and 42. Neurobiology of Disease, 20(1), 74–81. https://doi.org/10.1016/j.nbd.2005.02.003
   PubMed Web of Science ®Google Scholar
• Lobanov, M. Y., Bogatyreva, N., & Galzitskaya, O. (2008). Radius of gyration as an indicator of protein structure compactness. Molecular Biology, 42(4), 623–628. https://doi.org/10.1134/S0026893308040195
   Web of Science ®Google Scholar
• Locke, W. J., Guanzon, D., Ma, C., Liew, Y. J., Duesing, K. R., Fung, K. Y., & Ross, J. P. (2019). DNA methylation cancer biomarkers: Translation to the clinic. Frontiers in Genetics, 10, 1150. https://doi.org/10.3389/fgene.2019.01150
   PubMed Web of Science ®Google Scholar
• Lopes, F. M., Schröder, R., da Frota, M. L. C., Zanotto-Filho, A., Müller, C. B., Pires, A. S., Meurer, R. T., Colpo, G. D., Gelain, D. P., Kapczinski, F., Moreira, J. C. F., Fernandes, M. d C., & Klamt, F. (2010). Comparison between proliferative and neuron-like SH-SY5Y cells as an in vitro model for Parkinson disease studies. Brain Research, 1337, 85–94. https://doi.org/10.1016/j.brainres.2010.03.102
   PubMed Web of Science ®Google Scholar
• Lu, H., Su, H., Yang, B., & You, Q.-D. (2011). Design, synthesis, and biological activities of histone deacetylase inhibitors with diketo ester as zinc binding group. Yao Xue Xue Bao = Acta Pharmaceutica Sinica, 46(3), 293–298.
   PubMedGoogle Scholar
• Ma, C., & D'Mello, S. R. (2011). Neuroprotection by histone deacetylase-7 (HDAC7) occurs by inhibition of c-jun expression through a deacetylase-independent mechanism. The Journal of Biological Chemistry, 286(6), 4819–4828. https://doi.org/10.1074/jbc.M110.146860
   PubMed Web of Science ®Google Scholar
• Magalingam, K. B., Radhakrishnan, A., Ping, N. S., & Haleagrahara, N. (2018). Current concepts of neurodegenerative mechanisms in Alzheimer’s disease. BioMed Research International, 2018, 3740461–3740412. https://doi.org/10.1155/2018/3740461
   PubMed Web of Science ®Google Scholar
• Maiarù, M., Morgan, O. B., Tochiki, K. K., Hobbiger, E. J., Rajani, K., Overington, D. W., & Géranton, S. M. (2016). Complex regulation of the regulator of synaptic plasticity histone deacetylase 2 in the rodent dorsal horn after peripheral injury. Journal of Neurochemistry, 138(2), 222–232. https://doi.org/10.1111/jnc.13621
   PubMed Web of Science ®Google Scholar
• Mohseni, J., Al-Najjar, B. O., Wahab, H. A., Zabidi-Hussin, Z., & Sasongko, T. H. (2016). Transcript, methylation and molecular docking analyses of the effects of HDAC inhibitors, SAHA and Dacinostat, on SMN2 expression in fibroblasts of SMA patients. Journal of Human Genetics, 61(9), 823–830. https://doi.org/10.1038/jhg.2016.61
   PubMed Web of Science ®Google Scholar
• N Karpova, N., J Sales, A., & R Joca, S. (2017). Epigenetic basis of neuronal and synaptic plasticity. Current Topics in Medicinal Chemistry, 17(7), 771–793.
   PubMed Web of Science ®Google Scholar
• Omoruyi, S. I., Delport, J., Kangwa, T. S., Ibrakaw, A. S., Cupido, C. N., Ekpo, O. E., & Hussein, A. A. (2021). In vitro neuroprotective potential of Clivia miniata and Nerine humilis (Amaryllidaceae) in MPP+-induced neuronal toxicity in SH-SY5Y neuroblastoma cells. South African Journal of Botany, 136, 110–117. https://doi.org/10.1016/j.sajb.2020.06.028
   Web of Science ®Google Scholar
• Poli, G., Granchi, C., Rizzolio, F., & Tuccinardi, T. (2020). Application of MM-PBSA methods in virtual screening. Molecules (Basel, Switzerland), 25(8), 1971. https://doi.org/10.3390/molecules25081971
   PubMed Web of Science ®Google Scholar
• Prince, M. J. (2015). World Alzheimer Report 2015: The global impact of dementia: An analysis of prevalence, incidence, cost and trends. Alzheimer’s Disease International.
   Google Scholar
• Remiszewski, S. W., Sambucetti, L. C., Bair, K. W., Bontempo, J., Cesarz, D., Chandramouli, N., Chen, R., Cheung, M., Cornell-Kennon, S., Dean, K., Diamantidis, G., France, D., Green, M. A., Howell, K. L., Kashi, R., Kwon, P., Lassota, P., Martin, M. S., Mou, Y., … Atadja, P. (2003). N-Hydroxy-3-phenyl-2-propenamides as novel inhibitors of human histone deacetylase with in vivo antitumor activity: Discovery of (2 E)-N-hydroxy-3-[4-[[(2-hydroxyethyl)[2-(1 H-indol-3-yl) ethyl] amino] methyl] phenyl]-2-propenamide (NVP-LAQ824). Journal of Medicinal Chemistry, 46(21), 4609–4624. https://doi.org/10.1021/jm030235w
   PubMed Web of Science ®Google Scholar
• Reuter, S., Gupta, S. C., Park, B., Goel, A., & Aggarwal, B. B. (2011). Epigenetic changes induced by curcumin and other natural compounds. Genes & Nutrition, 6(2), 93–108. https://doi.org/10.1007/s12263-011-0222-1
   PubMed Web of Science ®Google Scholar
• Rylova, G., Ozdian, T., Varanasi, L., Soural, M., Hlavac, J., Holub, D., Dzubak, P., & Hajduch, M. (2015). Affinity-based methods in drug-target discovery. Current Drug Targets, 16(1), 60–76. https://doi.org/10.2174/1389450115666141120110323
   PubMed Web of Science ®Google Scholar
• Saha, R., & Pahan, K. (2006). HATs and HDACs in neurodegeneration: A tale of disconcerted acetylation homeostasis. Cell Death and Differentiation, 13(4), 539–550. https://doi.org/10.1038/sj.cdd.4401769
   PubMed Web of Science ®Google Scholar
• Santarelli, L., Saxe, M., Gross, C., Surget, A., Battaglia, F., Dulawa, S., Weisstaub, N., Lee, J., Duman, R., Arancio, O., Belzung, C., & Hen, R. (2003). Requirement of hippocampal neurogenesis for the behavioral effects of antidepressants. Science (New York, N.Y.), 301(5634), 805–809. https://doi.org/10.1126/science.1083328
   PubMed Web of Science ®Google Scholar
• Schrödinger, L., & DeLano, W. (2020). PyMOL. http://www.pymol.org/pymol
   Google Scholar
• Schuetz, A., Min, J., Allali-Hassani, A., Schapira, M., Shuen, M., Loppnau, P., Mazitschek, R., Kwiatkowski, N. P., Lewis, T. A., Maglathin, R. L., McLean, T. H., Bochkarev, A., Plotnikov, A. N., Vedadi, M., & Arrowsmith, C. H. (2008). Human HDAC7 harbors a class IIa histone deacetylase-specific zinc binding motif and cryptic deacetylase activity. The Journal of Biological Chemistry, 283(17), 11355–11363. https://doi.org/10.1074/jbc.M707362200
   PubMed Web of Science ®Google Scholar
• Seto, E., & Yoshida, M. (2014). Erasers of histone acetylation: The histone deacetylase enzymes. Cold Spring Harbor Perspectives in Biology, 6(4), a018713–a018713. https://doi.org/10.1101/cshperspect.a018713
   PubMed Web of Science ®Google Scholar
• Smilgies, D.-M., & Folta-Stogniew, E. (2015). Molecular weight–gyration radius relation of globular proteins: A comparison of light scattering, small-angle X-ray scattering and structure-based data. Journal of Applied Crystallography, 48(Pt 5), 1604–1606. https://doi.org/10.1107/S1600576715015551
   PubMedGoogle Scholar
• Tambunan, U. S. F., Bakri, R., Prasetia, T., Parikesit, A. A., & Kerami, D. (2013). Molecular dynamics simulation of complex histones deacetylase (HDAC) Class II Homo Sapiens with suberoylanilide hydroxamic acid (SAHA) and its derivatives as inhibitors of cervical cancer. Bioinformation, 9(13), 696–700. https://doi.org/10.6026/97320630009696
   PubMedGoogle Scholar
• Tsvetkova, D., Obreshkova, D., Zheleva-Dimitrova, D., & Saso, L. (2013). Antioxidant activity of galantamine and some of its derivatives. Current Medicinal Chemistry, 20(36), 4595–4608. https://doi.org/10.2174/09298673113209990148
   PubMed Web of Science ®Google Scholar
• Uba, A. I., & Zengin, G. (2023). In the quest for histone deacetylase inhibitors: Current trends in the application of multilayered computational methods. Amino Acids, 55(6),1–18. https://doi.org/10.1007/s00726-023-03297-y
   PubMedGoogle Scholar
• Van Der Spoel, D., Lindahl, E., Hess, B., Groenhof, G., Mark, A. E., & Berendsen, H. J. (2005). GROMACS: Fast, flexible, and free. Journal of Computational Chemistry, 26(16), 1701–1718. https://doi.org/10.1002/jcc.20291
   PubMed Web of Science ®Google Scholar
• Vanommeslaeghe, K., Hatcher, E., Acharya, C., Kundu, S., Zhong, S., Shim, J., Darian, E., Guvench, O., Lopes, P., Vorobyov, I., & Mackerell, A. D. (2010). CHARMM general force field: A force field for drug‐like molecules compatible with the CHARMM all‐atom additive biological force fields. Journal of Computational Chemistry, 31(4), 671–690. https://doi.org/10.1002/jcc.21367
   PubMed Web of Science ®Google Scholar
• Wang, S. C., Oelze, B., & Schumacher, A. (2008). Age-specific epigenetic drift in late-onset Alzheimer’s disease. PloS One, 3(7), e2698. https://doi.org/10.1371/journal.pone.0002698
   PubMed Web of Science ®Google Scholar
• Watson, P. J., Fairall, L., Santos, G. M., & Schwabe, J. W. R. (2012). Structure of HDAC3 bound to co-repressor and inositol tetraphosphate. Nature, 481(7381), 335–340. https://doi.org/10.1038/nature10728
   PubMed Web of Science ®Google Scholar
• Wu, H., Ichikawa, S., Tani, C., Zhu, B., Tada, M., Shimoishi, Y., Murata, Y., & Nakamura, Y. (2009). Docosahexaenoic acid induces ERK1/2 activation and neuritogenesis via intracellular reactive oxygen species production in human neuroblastoma SH-SY5Y cells. Biochimica et Biophysica Acta, 1791(1), 8–16. https://doi.org/10.1016/j.bbalip.2008.10.004
   PubMed Web of Science ®Google Scholar
• Zhu, H., Liu, J., V, K., C, G. P. D., Chakraborty, C., & Chen, L. (2015). Analysing the effect of mutation on protein function and discovering potential inhibitors of CDK4: Molecular modelling and dynamics studies. PloS One, 10(8), e0133969. https://doi.org/10.1371/journal.pone.0133969
   PubMed Web of Science ®Google Scholar
• Zhu, Y.-Y., Li, X., Yu, H.-Y., Xiong, Y.-F., Zhang, P., Pi, H.-F., & Ruan, H.-L. (2015). Alkaloids from the bulbs of Lycoris longituba and their neuroprotective and acetylcholinesterase inhibitory activities. Archives of Pharmacal Research, 38(5), 604–613. https://doi.org/10.1007/s12272-014-0397-2
   PubMed Web of Science ®Google Scholar