Investigation of HDAC8-ligands’ intermolecular forces through molecular dynamics simulations: profiling of non-bonding energies to design potential compounds as new anti-cancer agents

References

• Adhikari, N., Amin, S. A., & Jha, T. (2018). Selective and nonselective HDAC8 inhibitors: A therapeutic patent review. Pharmaceutical Patent Analyst, 7(6), 259–276. https://doi.org/10.4155/ppa-2018-0019
   PubMed Web of Science ®Google Scholar
• Arrowsmith, C. H., Bountra, C., Fish, P. V., Lee, K., & Schapira, M. (2012). Epigenetic protein families: A new frontier for drug discovery. Nature Reviews. Drug Discovery, 11(5), 384–400. https://doi.org/10.1038/nrd3674
   PubMed Web of Science ®Google Scholar
• Baker, N. A., Sept, D., Joseph, S., Holst, M. J., & McCammon, J. A. (2001). Electrostatics of nanosystems: Application to microtubules and the ribosome. Proceedings of the National Academy of Sciences of the United States of America, 98(18), 10037–10041. https://doi.org/10.1073/pnas.181342398
   PubMed Web of Science ®Google Scholar
• Balasubramanian, S., Verner, E., & Buggy, J. J. (2009). Isoform-specific histone deacetylase inhibitors: The next step? Cancer Letters, 280(2), 211–221. https://doi.org/10.1016/j.canlet.2009.02.013
   PubMed Web of Science ®Google Scholar
• Bayly, C. I., Cieplak, P., Cornell, W. D., & Kollman, P. A. (1993). A well-behaved electrostatic potential based method using charge restraints for deriving atomic charges: The RESP model. Journal of Physical Chemistry, 97(40), 10269-10280. https://doi.org/10.1021/j100142a004
   Google Scholar
• Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., Shindyalov, I. 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
• Bhansali, P., Hanigan, C. L., Perera, L., Casero, R. A., & Tillekeratne, L. M. V. (2014). Synthesis and biological evaluation of largazole analogues with modified surface recognition cap groups. European Journal of Medicinal Chemistry, 86, 528–541. https://doi.org/10.1016/j.ejmech.2014.09.009
   PubMed Web of Science ®Google Scholar
• Biasini, M., Bienert, S., Waterhouse, A., Arnold, K., Studer, G., Schmidt, T., Kiefer, F., Cassarino, T. G., Bertoni, M., Bordoli, L., & Schwede, T. (2014). SWISS-MODEL: Modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Research, 42(W1), W252–258. https://doi.org/10.1093/nar/gku340
   PubMed Web of Science ®Google Scholar
• Bieliauskas, A. V., & Pflum, M. K. H. (2008). Isoform-selective histone deacetylase inhibitors. Chemical Society Reviews, 37(7), 1402–1413. https://doi.org/10.1039/b703830p
   PubMed Web of Science ®Google Scholar
• Böhm, H. J., & Schneider, G. (2003). Protein‐ligand interactions. In H. ‐J. Böhm & G. Schneider (Eds.), Protein-ligand interactions: From molecular recognition to drug design. Wiley. https://doi.org/10.1002/3527601813
   Google Scholar
• Brooks, B. R., Bruccoleri, R. E., Olafson, B. D., States, D. J., Swaminathan, S., & Karplus, M. (1983). CHARMM: A program for macromolecular energy, minimization, and dynamics calculations. Journal of Computational Chemistry, 4(2), 187–217. https://doi.org/10.1002/jcc.540040211
   Web of Science ®Google Scholar
• Brunsteiner, M., & Petukhov, P. A. (2012). Insights from comprehensive multiple receptor docking to HDAC8. Journal of Molecular Modeling, 18(8), 3927–3939. https://doi.org/10.1007/s00894-011-1297-8
   PubMed Web of Science ®Google Scholar
• Chakrabarti, A., Oehme, I., Witt, O., Oliveira, G., Sippl, W., Romier, C., Pierce, R. J., & Jung, M. (2015). HDAC8: A multifaceted target for therapeutic interventions. Trends in Pharmacological Sciences, 36(7), 481–492. https://doi.org/10.1016/j.tips.2015.04.013
   PubMed Web of Science ®Google Scholar
• Chen, Y. C. (2015). Beware of docking!. Trends in Pharmacological Sciences, 36(2), 78–95. https://doi.org/10.1016/j.tips.2014.12.001
   PubMed Web of Science ®Google Scholar
• Cole, K. E., Dowling, D. P., Boone, M. A., Phillips, A. J., & Christianson, D. W. (2011). Structural basis of the antiproliferative activity of largazole, a depsipeptide inhibitor of the histone deacetylases. Journal of the American Chemical Society, 133(32), 12474–12477. https://doi.org/10.1021/ja205972n
   PubMed Web of Science ®Google Scholar
• Coordinators, N. R. (2017). Database resources of the national center for biotechnology information. Nucleic Acids Research, 45(D1), D12–D17. https://doi.org/10.1093/nar/gkw1071
   PubMed Web of Science ®Google Scholar
• Desai, A. G., Qazi, G. N., Ganju, R. K., El-Tamer, M., Singh, J., Saxena, A. K., Bedi, Y. S., Taneja, S. C., & Bhat, H. K. (2008). Medicinal plants and cancer chemoprevention. Current Drug Metabolism, 9(7), 581–591. https://doi.org/10.2174/138920008785821657
   PubMed Web of Science ®Google Scholar
• Deschamps, N., Simões-Pires, C. A., Carrupt, P. A., & Nurisso, A. (2015). How the flexibility of human histone deacetylases influences ligand binding: An overview. Drug Discovery Today, 20(6), 736–742. https://doi.org/10.1016/j.drudis.2015.01.004
   PubMed Web of Science ®Google Scholar
• Dewaker, V., Srivastava, P. N., Verma, S., & Prabhakar, Y. S. (2020). Molecular dynamics study of HDAC8-largazole analogues co-crystals for designing potential anticancer compounds. Journal of Biomolecular Structure & Dynamics, 38(4), 1197–1213. https://doi.org/10.1080/07391102.2019.1598497
   PubMed Web of Science ®Google Scholar
• Dokmanovic, M., & Marks, P. A. (2005). Prospects: Histone deacetylase inhibitors. Journal of Cellular Biochemistry, 96(2), 293–304. https://doi.org/10.1002/jcb.20532
   PubMed Web of Science ®Google Scholar
• Donini, O. A. T., & Kollman, P. A. (2000). Calculation and prediction of binding free energies for the matrix metalloproteinases. Journal of Medicinal Chemistry, 43(22), 4180–4188. https://doi.org/10.1021/jm000040d
   PubMed Web of Science ®Google Scholar
• Dowling, D. P., Gantt, S. L., Gattis, S. G., Fierke, C. A., & Christianson, D. W. (2008). Structural studies of human histone deacetylase 8 and its site-specific variants complexed with substrate and inhibitors. Biochemistry, 47(51), 13554–13563. https://doi.org/10.1021/bi801610c
   PubMed Web of Science ®Google Scholar
• Dowling, D. P., Gattis, S. G., Fierke, C. A., & Christianson, D. W. (2010). Structures of metal-substituted human histone deacetylase 8 provide mechanistic inferences on biological function. . Biochemistry, 49(24), 5048–5056. https://doi.org/10.1021/bi1005046
   PubMed Web of Science ®Google Scholar
• Estiu, G., West, N., Mazitschek, R., Greenberg, E., Bradner, J. E., & Wiest, O. (2010). On the inhibition of histone deacetylase 8. Bioorganic & Medicinal Chemistry, 18(11), 4103–4110. https://doi.org/10.1016/j.bmc.2010.03.080
   PubMed Web of Science ®Google Scholar
• Finnin, M. S., Donigian, J. R., Cohen, A., Richon, V. M., Rifkind, R. A., Marks, P. A., Breslow, R., & Pavletich, N. P. (1999). Structures of a histone deacetylase homologue bound to the TSA and SAHA inhibitors. Nature, 401(6749), 188–193. https://doi.org/10.1038/43710
   PubMed Web of Science ®Google Scholar
• Gallinari, P., Di Marco, S., Jones, P., Pallaoro, M., & Steinkühler, C. (2007). HDACs, histone deacetylation and gene transcription: From molecular biology to cancer therapeutics. Cell Research, 17(3), 195–211. https://doi.org/10.1038/sj.cr.7310149
   PubMed Web of Science ®Google Scholar
• Genheden, S., & Ryde, U. (2015). The MM/PBSA and MM/GBSA methods to estimate ligand-binding affinities. Expert Opinion on Drug Discovery, 10(5), 449–461. https://doi.org/10.1517/17460441.2015.1032936
   PubMed Web of Science ®Google Scholar
• Gordon, J. C., Myers, J. B., Folta, T., Shoja, V., Heath, L. S., & Onufriev, A. (2005). H++: A server for estimating pKas and adding missing hydrogens to macromolecules. Nucleic Acids Research, 33(Web Server), W368–371. https://doi.org/10.1093/nar/gki464
   PubMed Web of Science ®Google Scholar
• Greenwood, S. O. R., Chan, A. W. E., Hansen, D. F., & Marson, C. M. (2020). Potent non-hydroxamate inhibitors of histone deacetylase-8: Role and scope of an isoindolin-2-yl linker with an α-amino amide as the zinc-binding unit. Bioorganic & Medicinal Chemistry Letters, 30(5), 126926. https://doi.org/10.1016/j.bmcl.2019.126926
   PubMed Web of Science ®Google Scholar
• Grootenhuis, P. D. J., & van Galen, P. J. M. (1995). Correlation of binding affinities with non-bonded interaction energies of thrombin-inhibitor complexes. Acta Crystallographica. Section D, Biological Crystallography, 51(Pt 4), 560–566. https://doi.org/10.1107/S0907444994011686
   PubMedGoogle Scholar
• Hassanzadeh, M., Bagherzadeh, K., & Amanlou, M. (2016). A comparative study based on docking and molecular dynamics simulations over HDAC-tubulin dual inhibitors. Journal of Molecular Graphics & Modelling, 70, 170–180. https://doi.org/10.1016/j.jmgm.2016.10.007
   PubMed Web of Science ®Google Scholar
• Heringa, J., Higgins, D. G., & Notredame, C. (2000). T-Coffee: A novel method for fast and accurate multiple sequence alignment. Journal of Molecular Biology, 302(1), 205–217. https://doi.org/10.1006/jmbi.2000.4042
   PubMed Web of Science ®Google Scholar
• Hess-Stumpp, H. (2005). Histone deacetylase inhibitors and cancer: From cell biology to the clinic. European Journal of Cell Biology, 84(2-3), 109–121. https://doi.org/10.1016/j.ejcb.2004.12.010
   PubMed Web of Science ®Google Scholar
• Holloway, M. K., Wai, J. M., Halgren, T. A., Fitzgerald, P. M., Vacca, J. P., Dorsey, B. D., Levin, R. B., Thompson, W. J., Chen, L. J., & deSolms, S. J. (1995). A priori prediction of activity for HIV-1 protease inhibitors employing energy minimization in the active site. Journal of Medicinal Chemistry, 38(2), 305–317. https://doi.org/10.1021/jm00002a012
   PubMed Web of Science ®Google Scholar
• Huang, D., Li, X., & Xiu, Z. (2012). Molecular modeling of the interactions between histone deacetylase 8 and inhibitors. Journal of Theoretical and Computational Chemistry, 11(04), 907–924. https://doi.org/10.1142/S0219633612500617
   Web of Science ®Google Scholar
• Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14(1), 33–38. https://doi.org/10.1016/0263-7855(96)00018-5
   PubMedGoogle Scholar
• Kalyaanamoorthy, S., & Chen, Y. P. P. (2013). Energy based pharmacophore mapping of HDAC inhibitors against class i HDAC enzymes. Biochimica et Biophysica Acta, 1834(1), 317–328. https://doi.org/10.1016/j.bbapap.2012.08.009
   PubMed Web of Science ®Google Scholar
• Kashyap, K., & Kakkar, R. (2020). An insight into selective and potent inhibition of histone deacetylase 8 through induced-fit docking, pharmacophore modeling and QSAR studies. Journal of Biomolecular Structure & Dynamics, 38(1), 48–65. https://doi.org/10.1080/07391102.2019.1567388
   PubMed Web of Science ®Google Scholar
• Kassem, S., Ahmed, M., El-Sheikh, S., & Barakat, K. H. (2015). Entropy in bimolecular simulations: A comprehensive review of atomic fluctuations-based methods. Journal of Molecular Graphics & Modelling, 62, 105–117. https://doi.org/10.1016/j.jmgm.2015.09.010
   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., & Bryant, S. H. (2016). PubChem substance and compound databases. Nucleic Acids Research, 44(D1), D1202–D1213. https://doi.org/10.1093/nar/gkv951
   PubMed Web of Science ®Google Scholar
• KrennHrubec, K., Marshall, B. L., Hedglin, M., Verdin, E., & Ulrich, S. M. (2007). Design and evaluation of “Linkerless” hydroxamic acids as selective HDAC8 inhibitors. Bioorganic & Medicinal Chemistry Letters, 17(10), 2874–2878. https://doi.org/10.1016/j.bmcl.2007.02.064
   PubMed Web of Science ®Google Scholar
• Kroschinsky, F., Stölzel, F., von Bonin, S., Beutel, G., Kochanek, M., Kiehl, M., & Schellongowski, P. (2017). New drugs, new toxicities: Severe side effects of modern targeted and immunotherapy of cancer and their management. Critical Care, 21(1), 1–11. https://doi.org/10.1186/s13054-017-1678-1
   PubMed Web of Science ®Google Scholar
• Kunze, M. B. A., Wright, D. W., Werbeck, N. D., Kirkpatrick, J., Coveney, P. V., & Hansen, D. F. (2013). Loop interactions and dynamics tune the enzymatic activity of the human histone deacetylase 8. Journal of the American Chemical Society, 135(47), 17862–17868. https://doi.org/10.1021/ja408184x
   PubMed Web of Science ®Google Scholar
• Laskowski, R. A., MacArthur, M. W., Moss, D. S., & Thornton, J. M. (1993). PROCHECK: A program to check the stereochemical quality of protein structures. Journal of Applied Crystallography, 26(2), 283–291. https://doi.org/10.1107/S0021889892009944
   Web of Science ®Google Scholar
• Lee, J.-H., Choy, M. L., Ngo, L., Foster, S. S., & Marks, P. A. (2010). Histone deacetylase inhibitor induces DNA damage, which normal but not transformed cells can repair. Proceedings of the National Academy of Sciences of the United States of America, 107(33), 14639–14644. https://doi.org/10.1073/pnas.1008522107
   PubMed Web of Science ®Google Scholar
• Li, Y., Cong, Y., Feng, G., Zhong, S., Zhang, J. Z. H., Sun, H., & Duan, L. (2018). The impact of interior dielectric constant and entropic change on HIV-1 complex binding free energy prediction. Structural Dynamics (Melville, N.Y.), 5(6), 064101. https://doi.org/10.1063/1.5058172
   PubMed Web of Science ®Google Scholar
• Lipinski, C. A. (2000). Drug-like properties and the causes of poor solubility and poor permeability. Journal of Pharmacological and Toxicological Methods, 44(1), 235–249. https://doi.org/10.1016/S1056-8719(00)00107-6
   PubMed Web of Science ®Google Scholar
• Liu, H., & Hou, T. (2016). CaFE: A tool for binding affinity prediction using end-point free energy methods. Bioinformatics (Oxford, England)), 32(14), 2216–2218. https://doi.org/10.1093/bioinformatics/btw215
   PubMed Web of Science ®Google Scholar
• López, J. E., Sullivan, E. D., & Fierke, C. A. (2016). Metal-dependent deacetylases: Cancer and epigenetic regulators. ACS Chemical Biology, 11(3), 706–716. https://doi.org/10.1021/acschembio.5b01067
   PubMed Web of Science ®Google Scholar
• Manal, M., Chandrasekar, M. J. N., Gomathi Priya, J., & Nanjan, M. J. (2016). Inhibitors of histone deacetylase as antitumor agents: A critical review. Bioorganic Chemistry, 67, 18–42. https://doi.org/10.1016/j.bioorg.2016.05.005
   PubMed Web of Science ®Google Scholar
• Maret, W., & Li, Y. (2009). Coordination dynamics of zinc in proteins. Chemical Reviews, 109(10), 4682–4707. https://doi.org/10.1021/cr800556u
   PubMed Web of Science ®Google Scholar
• Marks, P. a., & Dokmanovic, M. (2005). Histone deacetylase inhibitors: Discovery and development as anticancer agents. Expert Opinion on Investigational Drugs, 14(12), 1497–1511. https://doi.org/10.1517/13543784.14.12.1497
   PubMed Web of Science ®Google Scholar
• Micelli, C., & Rastelli, G. (2015). Histone deacetylases: Structural determinants of inhibitor selectivity. Drug Discovery Today, 20(6), 718–735. https://doi.org/10.1016/j.drudis.2015.01.007
   PubMed Web of Science ®Google Scholar
• Miller, B. R., McGee, T. D., Swails, J. M., Homeyer, N., Gohlke, H., & Roitberg, A. E. (2012). MMPBSA.py: An efficient program for end-state free energy calculations. Journal of Chemical Theory and Computation, 8(9), 3314–3321. https://doi.org/10.1021/ct300418h
   PubMed Web of Science ®Google Scholar
• Miller, K. D., Nogueira, L., Mariotto, A. B., Rowland, J. H., Yabroff, K. R., Alfano, C. M., Jemal, A., Kramer, J. L., & Siegel, R. L. (2019). Cancer treatment and survivorship statistics, 2019. CA: A Cancer Journal for Clinicians, 69(5), 363–385. https://doi.org/10.3322/caac.21565
   PubMed Web of Science ®Google Scholar
• Molecular Operating Environment (MOE), Version. (2008). Chemical Computing Group Inc.: Montreal, Quebec, Canada, 2008. http://www.chemcomp.com.
   Google Scholar
• New, M., Olzscha, H., & La Thangue, N. B. (2012). HDAC inhibitor-based therapies: Can we interpret the code? Molecular Oncology, 6(6), 637–656. https://doi.org/10.1016/j.molonc.2012.09.003
   PubMed Web of Science ®Google Scholar
• Pettersen, E. F., Goddard, T. D., Huang, C. C., Couch, G. S., Greenblatt, D. M., Meng, E. C., & Ferrin, T. E. (2004). UCSF Chimera-a visualization system for exploratory research and analysis. Journal of Computational Chemistry, 25(13), 1605–1612. https://doi.org/10.1002/jcc.20084
   PubMed Web of Science ®Google Scholar
• Phillips, J. C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R. D., Kalé, L., & Schulten, K. (2005). Scalable molecular dynamics with NAMD. Journal of Computational Chemistry, 26(16), 1781–1802. https://doi.org/10.1002/jcc.20289
   PubMed Web of Science ®Google Scholar
• Phillips, J., Hardy, D., Isgro, T., Phillips, J., Villa, E., Yu, H., … Hardy, D. (2017). Namd Tutorial. (April), 1–120.
   Google Scholar
• Porter, N. J., Christianson, N. H., Decroos, C., & Christianson, D. W. (2016). Structural and functional influence of the glycine-rich loop G302GGGY on the catalytic tyrosine of histone deacetylase 8. Biochemistry, 55(48), 6718–6729. https://doi.org/10.1021/acs.biochem.6b01014
   PubMed Web of Science ®Google Scholar
• Prasad, V., De Jesús, K., & Mailankody, S. (2017). The high price of anticancer drugs: Origins, implications, barriers, solutions. Nature Reviews. Clinical Oncology, 14(6), 381–390. https://doi.org/10.1038/nrclinonc.2017.31
   PubMed Web of Science ®Google Scholar
• Qin, H. T., Li, H. Q., & Liu, F. (2017). Selective histone deacetylase small molecule inhibitors: Recent progress and perspectives. Expert Opinion on Therapeutic Patents, 27(5), 621–636. https://doi.org/10.1080/13543776.2017.1276565
   PubMed Web of Science ®Google Scholar
• Sixto-López, Y., Bello, M., & Correa-Basurto, J. (2018a). Insights into structural features of HDAC1 and its selectivity inhibition elucidated by Molecular dynamic simulation and Molecular Docking. Journal of Biomolecular Structure & Dynamics, 37(3), 584–610. https://doi.org/10.1080/07391102.2018.1441072
   PubMed Web of Science ®Google Scholar
• Sixto-López, Y., Bello, M., & Correa-Basurto, J. (2018b). Structural and energetic basis for the inhibitory selectivity of both catalytic domains of dimeric HDAC6. Journal of Biomolecular Structure and Dynamics, 37(18), 4701–4720. https://doi.org/10.1080/07391102.2018.1557560
   Web of Science ®Google Scholar
• Sixto-López, Y., Bello, M., & Correa-Basurto, J. (2020). Exploring the inhibitory activity of valproic acid against the HDAC family using an MMGBSA approach. Journal of Computer-Aided Molecular Design, (I). https://doi.org/10.1007/s10822-020-00304-2
   Google Scholar
• Somoza, J. R., Skene, R. J., Katz, B. A., Mol, C., Ho, J. D., Jennings, A. J., Luong, C., Arvai, A., Buggy, J. J., Chi, E., Tang, J., Sang, B.-C., Verner, E., Wynands, R., Leahy, E. M., Dougan, D. R., Snell, G., Navre, M., Knuth, M. W., … Tari, L. W. (2004). Structural snapshots of human HDAC8 provide insights into the class I histone deacetylases. Structure (London, England : 1993)), 12(7), 1325–1334. https://doi.org/10.1016/j.str.2004.04.012
   PubMed Web of Science ®Google Scholar
• Stote, R. H., & Karplus, M. (1995). Zinc binding in proteins and solution: A simple but accurate nonbonded representation. Proteins, 23(1), 12–31. https://doi.org/10.1002/prot.340230104
   PubMed Web of Science ®Google Scholar
• Tabackman, A. A., Frankson, R., Marsan, E. S., Perry, K., & Cole, K. E. (2016). Structure of “ 'linkerless' hydroxamic acid inhibitor-HDAC8 complex confirms the formation of an isoform-specific subpocket” . Journal of Structural Biology, 195(3), 373–378. https://doi.org/10.1016/j.jsb.2016.06.023
   PubMed Web of Science ®Google Scholar
• Thaler, F., & Mercurio, C. (2014). Towards selective inhibition of histone deacetylase isoforms: What has been achieved, where we are and what will be next. ChemMedChem., 9(3), 523–536. https://doi.org/10.1002/cmdc.201300413
   PubMed Web of Science ®Google Scholar
• Thangapandian, S., John, S., & Lee, K. W. (2012). Molecular dynamics simulation study explaining inhibitor selectivity in different class of histone deacetylases. Journal of Biomolecular Structure & Dynamics, 29(4), 677–698. https://doi.org/10.1080/07391102.2012.10507409
   PubMed Web of Science ®Google Scholar
• Tilekar, K., Upadhyay, N., Jänsch, N., Schweipert, M., Mrowka, P., Meyer-Almes, F. J., & Ramaa, C. S. (2020). Discovery of 5-naphthylidene-2,4-thiazolidinedione derivatives as selective HDAC8 inhibitors and evaluation of their cytotoxic effects in leukemic cell lines. Bioorganic Chemistry, 95(October 2019), 103522. https://doi.org/10.1016/j.bioorg.2019.103522
   PubMed Web of Science ®Google Scholar
• Trot, O., & Olson, A. (2010). AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 31(2), 455–461. https://doi.org/10.1002/jcc https://doi.org/10.1002/jcc.21334
   PubMed Web of Science ®Google Scholar
• Uba, A. I., & Yelekçi, K. (2017). Identification of potential isoform-selective histone deacetylase inhibitors for cancer therapy: A combined approach of structure-based virtual screening, ADMET prediction and molecular dynamics simulation assay. Journal of Biomolecular Structure and Dynamics, 1102, 1–15. https://doi.org/10.1080/07391102.2017.1384402
   Google Scholar
• Vannini, A., Volpari, C., Filocamo, G., Casavola, E. C., Brunetti, M., Renzoni, D., Chakravarty, P., Paolini, C., De Francesco, R., Gallinari, P., Steinkühler, C., & Di Marco, S. (2004). Crystal structure of a eukaryotic zinc-dependent histone deacetylase, human HDAC8, complexed with a hydroxamic acid inhibitor. Proceedings of the National Academy of Sciences of the United States of America, 101(42), 15064–15069. https://doi.org/10.1073/pnas.0404603101
   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 https://doi.org/10.1002/jcc.21367
   PubMed Web of Science ®Google Scholar
• Vasiliauskaité-Brooks, I., Sounier, R., Rochaix, P., Bellot, G., Fortier, M., Hoh, F., De Colibus, L., Bechara, C., Saied, E. M., Arenz, C., Leyrat, C., & Granier, S. (2017). Structural insights into adiponectin receptors suggest ceramidase activity. Nature, 544(7648), 120–123. https://doi.org/10.1038/nature21714
   PubMed Web of Science ®Google Scholar
• Wang, C., Greene, D., Xiao, L., Qi, R., & Luo, R.(2018). Recent developments and applications of the MMPBSA method. Frontiers in Molecular Biosciences, 4(87), 1–18. https://doi.org/10.3389/fmolb.2017.00087
   Google Scholar
• Wang, J., Wang, W., Kollman, P. A., & Case, D. A. (2006). Automatic atom type and bond type perception in molecular mechanical calculations. Journal of Molecular Graphics & Modelling, 25(2), 247–260. https://doi.org/10.1016/j.jmgm.2005.12.005
   PubMed Web of Science ®Google Scholar
• Weerasinghe, S. V. W., Estiu, G., Wiest, O., & Pflum, M. K. H. (2008). Residues in the 11 angstrom channel of histone deacetylase 1 promote catalytic activity: Implications for designing isoform-selective HDAC inhibitors. Journal of Medicinal Chemistry, 51(18), 5542–5551. https://doi.org/10.1021/jm800081j236
   PubMed Web of Science ®Google Scholar
• Whitehead, L., Dobler, M. R., Radetich, B., Zhu, Y., Atadja, P. W., Claiborne, T., Grob, J. E., McRiner, A., Pancost, M. R., Patnaik, A., Shao, W., Shultz, M., Tichkule, R., Tommasi, R. A., Vash, B., Wang, P., & Stams, T. (2011). Human HDAC isoform selectivity achieved via exploitation of the acetate release channel with structurally unique small molecule inhibitors. Bioorganic & Medicinal Chemistry, 19(15), 4626–4634. https://doi.org/10.1016/j.bmc.2011.06.030
   PubMed Web of Science ®Google Scholar
• WHO. (2018). WHO | Cancer. Retrieved November 1, 2018, from http://www.who.int/cancer/en/
   Google Scholar
• Wiederstein, M., & Sippl, M. J. (2007). ProSA-web: Interactive web service for the recognition of errors in three-dimensional structures of proteins. Nucleic Acids Research, 35(Web Server), W407–410. https://doi.org/10.1093/nar/gkm290
   PubMed Web of Science ®Google Scholar
• Wu, R., Hu, P., Wang, S., Cao, Z., & Zhang, Y. (2010). Flexibility of catalytic zinc coordination in thermolysin and HDAC8: A Born-Oppenheimer ab initio QM/MM molecular dynamics study. Journal of Chemical Theory and Computation, 6(1), 337–343. https://doi.org/10.1021/ct9005322
   Web of Science ®Google Scholar
• Yan, C., Xiu, Z., Li, X., Li, S., Hao, C., & Teng, H. (2008). Comparative molecular dynamics simulations of histone deacetylase-like protein: Binding modes and free energy analysis to hydroxamic acid inhibitors. Proteins, 73(1), 134–149. https://doi.org/10.1002/prot.22047
   PubMed Web of Science ®Google Scholar
• Yang, T., Wu, J. C., Yan, C., Wang, Y., Luo, R., Gonzales, M. B., Dalby, K. N., & Ren, P. (2011). Virtual screening using molecular simulations. Proteins, 79(6), 1940–1951. https://doi.org/10.1002/prot.23018
   PubMed Web of Science ®Google Scholar
• Yu, Z., Li, P., & Merz, K. M. (2018). Extended Zinc AMBER Force Field (EZAFF). Journal of Chemical Theory and Computation, 14(1), 242–254. https://doi.org/10.1021/acs.jctc.7b00773
   PubMed Web of Science ®Google Scholar
• Zhou, H., Wang, C., Deng, T., Tao, R., & Li, W. (2018). Novel urushiol derivatives as HDAC8 inhibitors: Rational design, virtual screening, molecular docking and molecular dynamics studies. Journal of Biomolecular Structure & Dynamics, 36(8), 1966–1978. https://doi.org/10.1080/07391102.2017.1344568
   PubMed Web of Science ®Google Scholar