Molecular dynamics study of HDAC8-largazole analogues co-crystals for designing potential anticancer compounds

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. doi:10.4155/ppa-2018-0019
   PubMed Web of Science ®Google Scholar
• Almaliti, J., Al-Hamashi, A. A., Negmeldin, A. T., Hanigan, C. L., Perera, L., Pflum, M. K. H., … Tillekeratne, L. M. V. (2016). Largazole analogues embodying radical changes in the depsipeptide ring: Development of a more selective and highly potent analogue. Journal of Medicinal Chemistry, 59(23), 10642–10660. doi:10.1021/acs.jmedchem.6b01271
   PubMed Web of Science ®Google Scholar
• Amin, S. A., Adhikari, N., & Jha, T. (2017a). Is dual inhibition of metalloenzymes HDAC-8 and MMP-2 a potential pharmacological target to combat hematological malignancies? Pharmacological Research, 122, 8–19. doi:10.1016/j.phrs.2017.05.002
   PubMed Web of Science ®Google Scholar
• Amin, S. A., Adhikari, N., & Jha, T. (2017b). Structure-activity relationships of hydroxamate-based histone deacetylase-8 inhibitors: Reality behind anticancer drug discovery. Future Medicinal Chemistry, 9(18), 2211–2237. doi:10.4155/fmc-2017-0130
   PubMed Web of Science ®Google Scholar
• Amin, S. A., Adhikari, N., & Jha, T. (2018a). Diverse classes of HDAC8 inhibitors: In search of molecular fingerprints that regulate activity. Future Medicinal Chemistry, 10(13), 1589–1602. doi:10.4155/fmc-2018-0005
   PubMed Web of Science ®Google Scholar
• Amin, S. A., Adhikari, N., & Jha, T. (2018b). Structure-activity relationships of HDAC8 inhibitors: Non-hydroxamates as anticancer agents. Pharmacological Research. Amsterdam, The Netherlands: Elsevier Ltd. https://doi.org/10.1016/j.phrs.2018.03.001
   Google Scholar
• Amin, S. A., Bhargava, S., Adhikari, N., Gayen, S., & Jha, T. (2018). Exploring pyrazolo[3,4-d]pyrimidine phosphodiesterase 1 (PDE1) inhibitors: A predictive approach combining comparative validated multiple molecular modelling techniques. Journal of Biomolecular Structure and Dynamics, 36(3), 590–608. doi:10.1080/07391102.2017.1288659
   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. doi:10.1038/nrd3674
   PubMed Web of Science ®Google Scholar
• Banerjee, S., Adhikari, N., Amin, S. A., & Jha, T. (2019). Histone deacetylase 8 (HDAC8) and its inhibitors with selectivity to other isoforms: An overview. European Journal of Medicinal Chemistry, 164, 214–240. doi:10.1016/j.ejmech.2018.12.039
   PubMed Web of Science ®Google Scholar
• Berman, H. M., Westbrook, J., Feng, Z., Gilliland, G., Bhat, T. N., Weissig, H., … Bourne, P. E. (2000). The protein data bank. Nucleic Acids Research, 28(1), 235–242. doi: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. doi: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., … Schwede, T. (2014). SWISS-MODEL: Modelling protein tertiary and quaternary structure using evolutionary information. Nucleic Acids Research, 42(W1), 252–258. https://doi.org/10.1093/nar/gku340
   PubMed Web of Science ®Google Scholar
• Bowers, A. A., Greshock, T. J., West, N., Estiu, G., Schreiber, S. L., Wiest, O., … Bradner, J. E. (2009). Synthesis and conformation-activity relationships of the peptide isosteres of FK228 and largazole. Journal of the American Chemical Society, 131(8), 2900–2905. doi:10.1021/ja807772w
   PubMed Web of Science ®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. doi:10.1002/jcc.540040211
   Web of Science ®Google Scholar
• Chakrabarti, A., Melesina, J., Kolbinger, F. R., Oehme, I., Senger, J., Witt, O., … Jung, M. (2016). Targeting histone deacetylase 8 as a therapeutic approach to cancer and neurodegenerative diseases. Future Medicinal Chemistry, 8(13), 1609–1634. doi:10.4155/fmc-2016-0117
   PubMed Web of Science ®Google Scholar
• Chakrabarti, A., Oehme, I., Witt, O., Oliveira, G., Sippl, W., Romier, C., … Jung, M. (2015). HDAC8: A multifaceted target for therapeutic interventions. Trends in Pharmacological Sciences, 36(7), 481–492. doi:10.1016/j.tips.2015.04.013
   PubMed Web of Science ®Google Scholar
• Chen, F., Chai, H., Su, M. B., Zhang, Y. M., Li, J., Xie, X., & Nan, F. J. (2014). Potent and orally efficacious bisthiazole-based histone deacetylase inhibitors. ACS Medicinal Chemistry Letters, 5(6), 628–633. doi:10.1021/ml400470s
   PubMed Web of Science ®Google Scholar
• Chen, Y. C. (2015). Beware of docking! Trends in Pharmacological Sciences, 36(2), 78–95. doi:10.1016/j.tips.2014.12.001
   PubMed Web of Science ®Google Scholar
• Clausen, D. J., Smith, W. B., Haines, B. E., Wiest, O., Bradner, J. E., & Williams, R. M. (2015). Modular synthesis and biological activity of pyridyl-based analogs of the potent class I histone deacetylase inhibitor largazole. Bioorganic and Medicinal Chemistry, 23(15), 5061–5074. doi:10.1016/j.bmc.2015.03.063
   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. doi:10.1021/ja205972n
   PubMed Web of Science ®Google Scholar
• Colovos, C., & Yeates, T. O. (1993). Verification of protein structures: Patterns of nonbonded atomic interactions. Protein Science, 2(9), 1511–1519. doi:10.1002/pro.5560020916
   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
   Google Scholar
• Cragg, G. M., & Newman, D. J. (2013). Natural products: A continuing source of novel drug leads. Biochimica et Biophysica Acta - General Subjects, 1830(6), 3670–3695. doi:10.1016/j.bbagen.2013.02.008
   PubMed Web of Science ®Google Scholar
• Decroos, C., Clausen, D. J., Haines, B. E., Wiest, O., Williams, R. M., & Christianson, D. W. (2015). Variable active site loop conformations accommodate the binding of macrocyclic largazole analogues to HDAC8. Biochemistry, 54(12), 2126–2135. doi:10.1021/acs.biochem.5b00010
   PubMed Web of Science ®Google Scholar
• Desai, A., Qazi, G., Ganju, R., El-Tamer, M., Singh, J., Saxena, A., … Bhat, H. (2008). Medicinal plants and cancer chemoprevention. Current Drug Metabolism, 9(7), 581–591. https://doi.org/10.1037/a0013262.Open doi: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. doi:10.1016/j.drudis.2015.01.004
   PubMed Web of Science ®Google Scholar
• Dos Santos Passos, C., Simões-Pires, C. A., Carrupt, P. A., & Nurisso, A. (2016). Molecular dynamics of zinc-finger ubiquitin binding domains: A comparative study of histone deacetylase 6 and ubiquitin-specific protease 5. Journal of Biomolecular Structure and Dynamics, 34(12), 2581–2598. doi:10.1080/07391102.2015.1124051
   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. doi:10.1021/bi801610c
   PubMed Web of Science ®Google Scholar
• Durrant, J., & McCammon, J. A. (2011). Molecular dynamics simulations and drug discovery. BMC Biology, 9(71), 71–79. https://doi.org/10.1002/cber.18940270364 doi:10.1186/1741-7007-9-71
   PubMed Web of Science ®Google Scholar
• Engene, N., Tronholm, A., Salvador-Reyes, L. A., Luesch, H., & Paul, V. J. (2015). Caldora penicillata gen. nov., comb. nov. (Cyanobacteria), a pantropical marine species with biomedical relevance. Journal of Phycology, 51(4), 670–681. doi:10.1111/jpy.12309
   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. doi:10.1038/sj.cr.7310149
   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(Suppl 2), 368–371. https://doi.org/10.1093/nar/gki464
   Web of Science ®Google Scholar
• Hong, J., & Luesch, H. (2012). Largazole: From discovery to broad-spectrum therapy. Natural Product Reports, 29(4), 449. doi:10.1039/c2np00066k
   PubMed Web of Science ®Google Scholar
• Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14(1), 33–38. doi:10.1016/0263-7855(96)00018-5
   Google Scholar
• Ingham, O. J., Paranal, R. M., Smith, W. B., Escobar, R. A., Yueh, H., Snyder, T., … Beeler, A. B. (2016). Development of a potent and selective HDAC8 inhibitor. ACS Medicinal Chemistry Letters, 7(10), 929–932. doi:10.1021/acsmedchemlett.6b00239
   PubMed Web of Science ®Google Scholar
• Kashyap, K., & Kakkar, R. (2019). An insight into selective and potent inhibition of histone deacetylase 8 through induced-fit docking, pharmacophore modeling and QSAR studies. Journal of Biomolecular Structure and Dynamics, 1. doi:10.1080/07391102.2019.1567388
   PubMed Web of Science ®Google Scholar
• Katz, L., & Baltz, R. H. (2016). Natural product discovery: Past, present, and future. Journal of Industrial Microbiology & Biotechnology, 43(2-3), 155–176. doi:10.1007/s10295-015-1723-5
   PubMed Web of Science ®Google Scholar
• Kim, B., Ratnayake, R., Lee, H., Shi, G., Zeller, S. L., Li, C., … Hong, J. (2017). Synthesis and biological evaluation of largazole zinc-binding group analogs. Bioorganic and Medicinal Chemistry, 25(12), 3077–3086. doi:10.1016/j.bmc.2017.03.071
   PubMed Web of Science ®Google Scholar
• Kim, S., Thiessen, P. A., Bolton, E. E., Chen, J., Fu, G., Gindulyte, A., … Bryant, S. H. (2016). PubChem substance and compound databases. Nucleic Acids Research, 44(D1), D1202–D1213. doi:10.1093/nar/gkv951
   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 loop interactions and dynamics tune the enzymatic activity of the human histone deacetylase 8. Journal of the American Chemical Society, 135(47), 17862–17868. doi:10.1021/ja408184x
   PubMed Web of Science ®Google Scholar
• Lane, A. A., & Chabner, B. A. (2009). Histone deacetylase inhibitors in cancer therapy. Journal of Clinical Oncology, 27(32), 5459–5468. doi:10.1200/JCO.2009.22.1291
   PubMed Web of Science ®Google Scholar
• Laskowski, R. A. (2009). PDBsum new things. Nucleic Acids Research, 37(Suppl. 1), 355–359. https://doi.org/10.1093/nar/gkn860
   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. doi: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 United States of America, 107(33), 14639–14644. doi:10.1073/pnas.1008522107
   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 doi:10.1016/S1056-8719(00)00107-6
   PubMed Web of Science ®Google Scholar
• Mahalakshmi, R., Husayn Ahmed, P., & Mahadevan, V. (2018). HDAC inhibitors show differential epigenetic regulation and cell survival strategies on p53 mutant colon cancer cells. Journal of Biomolecular Structure and Dynamics, 36(4), 938–955. doi:10.1080/07391102.2017.1302820
   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. doi:10.1016/j.bioorg.2016.05.005
   PubMed Web of Science ®Google Scholar
• Molecular Operating Environment (MOE), Version. (2008). Molecular operating environment (MOE), version. Montreal, Quebec, Canada: Chemical Computing Group Inc. http://www.chemcomp.com.
   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. doi:10.1002/jcc.20084
   PubMed Web of Science ®Google Scholar
• Phillips, J. C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., … Schulten, K. (2005). Scalable molecular dynamics with NAMD. Journal of Computational Chemistry, 26(16), 1781–1802. doi: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
• Pilon, J. L., Clausen, D. J., Hansen, R. J., Lunghofer, P. J., Charles, B., Rose, B. J., … Williams, R. M. (2015). Comparative pharmacokinetic properties and antitumor activity of the marine HDACi Largazole and Largazole peptide isostere. Cancer Chemotherapy and Pharmacology, 75(4), 671–682. doi:10.1007/s00280-015-2675-1
   PubMed Web of Science ®Google Scholar
• Poli, G., Di Fabio, R., Ferrante, L., Summa, V., Botta, M., & Poli, G. (2017). Largazole analogues as histone deacetylase inhibitors and anticancer agents: An overview of structure-activity relationships. ChemMedChem, 12(23), 1917–1926. doi:10.1002/cmdc.201700563
   PubMed Web of Science ®Google Scholar
• Porter, N. J., & Christianson, D. W. (2017). Binding of the microbial cyclic tetrapeptide trapoxin A to the class I histone deacetylase HDAC8. ACS Chemical Biology, 12(9), 2281–2286. doi:10.1021/acschembio.7b00330
   PubMed Web of Science ®Google Scholar
• Salvador-Reyes, L. A., & Luesch, H. (2015). Biological targets and mechanisms of action of natural products from marine cyanobacteria. Natural Product Reports, 32(3), 478–503. doi:10.1039/C4NP00104D
   PubMed Web of Science ®Google Scholar
• Saxena, R., Chandra, V., Manohar, M., Hajela, K., Debnath, U., Prabhakar, Y. S., … Dwivedi, A. (2013). Chemotherapeutic potential of 2-[piperidinoethoxyphenyl]-3-phenyl-2h-benzo(b)pyran in estrogen receptor- negative breast cancer cells: Action via prevention of EGFR activation and combined inhibition of PI-3-K/Akt/FOXO and MEK/Erk/AP-1 pathways. PLoS One, 8(6). https://doi.org/10.1371/journal.pone.0066246
   Web of Science ®Google Scholar
• Saxena, R., Gupta, G., Manohar, M., Debnath, U., Popli, P., Prabhakar, Y. S., … Dwivedi, A. (2016). Spiro-oxindole derivative 5-chloro-4′,5′-diphenyl-3′-(4-(2-(piperidin-1-yl) ethoxy) benzoyl) spiro[indoline-3,2′-pyrrolidin]-2-one triggers apoptosis in breast cancer cells via restoration of p53 function. International Journal of Biochemistry and Cell Biology, 70, 105–117. doi:10.1016/j.biocel.2015.11.003
   PubMed Web of Science ®Google Scholar
• Shigematsu, N., Ueda, H., Takase, S., Tanaka, H., Yamamoto, K., & Tada, T. (1994). FR901228, a novel antitumor bicyclic depsipeptide produced by Chromobacterium violaceum no. 968. II. Structure determination. The Journal of Antibiotics, 47(3), 311–314. doi:10.7164/antibiotics.47.311
   PubMed Web of Science ®Google Scholar
• Sinha, S., Tyagi, C., Goyal, S., Jamal, S., Somvanshi, P., & Grover, A. (2016). Fragment based G-QSAR and molecular dynamics based mechanistic simulations into hydroxamic-based HDAC inhibitors against spinocerebellar ataxia. Journal of Biomolecular Structure and Dynamics, 34(10), 2281–2295. doi:10.1080/07391102.2015.1113386
   PubMed Web of Science ®Google Scholar
• Sixto-López, Y., Bello, M., Rodríguez-Fonseca, R. A., Gómez-Vidal, J. A., Correa-Basurto, J., Bello, M., … Martínez-Archundia, M. (2017). Searching the conformational complexity and binding properties of HDAC6 through docking and molecular dynamic simulations. Journal of Biomolecular Structure and Dynamics, 35(13), 2794–2814. doi:10.1080/07391102.2016.1231084
   PubMed Web of Science ®Google Scholar
• Sixto-López, Y., Bello, M., & Correa-Basurto, J. (2019). Insights into structural features of HDAC1 and its selectivity inhibition elucidated by molecular dynamic simulation and molecular docking. Journal of Biomolecular Structure and Dynamics, 37(3), 584–610. doi:10.1080/07391102.2018.1441072
   PubMed Web of Science ®Google Scholar
• Sixto-López, Y., Bello, M., & Correa-Basurto, J. (2018). Structural and energetic basis for the inhibitory selectivity of both catalytic domains of dimeric HDAC6. Journal of Biomolecular Structure and Dynamics, 1. doi:10.1080/07391102.2018.1557560
   PubMed Web of Science ®Google Scholar
• Somoza, J. R., Skene, R. J., Katz, B. A., Mol, C., Ho, J. D., Jennings, A. J., … Tari, L. W. (2004). Structural snapshots of human HDAC8 provide insights into the class I histone deacetylases. Structure, 12(7), 1325–1334. doi:10.1016/j.str.2004.04.012
   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
• Tan, S., & Liu, Z.-P. (2015). Natural products as zinc-dependent histone deacetylase inhibitors. ChemMedChem, 10(3), 441–450. doi:10.1002/cmdc.201402460
   PubMed Web of Science ®Google Scholar
• Taori, K., Paul, V. J., & Luesch, H. (2008). Structure and activity of largazole, a potent antiproliferative agent from the Floridian marine cyanobacterium Symploca sp. Journal of the American Chemical Society, 130(6), 1806–1807. doi:10.1021/ja7110064
   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 and Dynamics, 29(4), 677–698. doi:10.1080/07391102.2012.10507409
   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. doi:10.1002/jcc.21334
   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
• Uba, A. I., & Yelekçi, K. (2019). Homology modeling of human histone deacetylase 10 and design of potential selective inhibitors. Journal of Biomolecular Structure and Dynamics. doi:10.1080/07391102.2018.1521747
   Web of Science ®Google Scholar
• Vannini, A., Volpari, C., Filocamo, G., Casavola, E. C., Brunetti, M., Renzoni, D., … 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 United States of America, 101(42), 15064–15069. doi:10.1073/pnas.0404603101
   PubMed Web of Science ®Google Scholar
• Vannini, A., Volpari, C., Gallinari, P., Jones, P., Mattu, M., Carfí, A., … Di Marco, S. (2007). Substrate binding to histone deacetylases as shown by the crystal structure of the HDAC8-substrate complex. EMBO Reports, 8(9), 879–884. doi:10.1038/sj.embor.7401047
   PubMed Web of Science ®Google Scholar
• Vanommeslaeghe, K., Hatcher, E., Acharya, C., Kundu, S., Zhong, S., Shim, J., & Darian, E. (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, 671–690. https://doi.org/10.1002/jcc
   PubMed Web of Science ®Google Scholar
• Verma, S., & Prabhakar, Y. S. (2015). Target based drug design - A reality in virtual sphere. Current Medicinal Chemistry, 22(13), 1603–1630. doi:10.2174/0929867322666150209151209
   PubMed Web of Science ®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 and Modelling, 25(2), 247–260. doi:10.1016/j.jmgm.2005.12.005
   PubMed Web of Science ®Google Scholar
• Wang, Y., Yang, L., Hou, J., Zou, Q., Gao, Q., Yao, W., … Zhang, J. (2019). Hierarchical virtual screening of the dual MMP-2/HDAC-6 inhibitors from natural products based on pharmacophore models and molecular docking. Journal of Biomolecular Structure and Dynamics, 37(3), 649–670. doi:10.1080/07391102.2018.1434833
   PubMed Web of Science ®Google Scholar
• Whitehead, L., Dobler, M. R., Radetich, B., Zhu, Y., Atadja, P. W., Claiborne, T., … Stams, T. (2011). Human HDAC isoform selectivity achieved via exploitation of the acetate release channel with structurally unique small molecule inhibitors. Bioorganic and Medicinal Chemistry, 19(15), 4626–4634. doi: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(Suppl 2), 407–410. https://doi.org/10.1093/nar/gkm290
   PubMed Web of Science ®Google Scholar
• Ying, Y., Taori, K., Kim, H., Hong, J., & Luesch, H. (2008). Total synthesis and molecular target of largazole, a histone deacetylase inhibitor. Journal of the American Chemical Society, 130(26), 8455–8459. doi:10.1021/ja8013727
   PubMed Web of Science ®Google Scholar
• Yuan, Y., Hu, Z., Bao, M., Sun, R., Long, X., Long, L., … Bao, J. (2018). Screening of novel histone deacetylase 7 inhibitors through molecular docking followed by a combination of molecular dynamics simulations and ligand-based approach. Journal of Biomolecular Structure and Dynamics, 1. doi:10.1080/07391102.2018.1541141
   PubMed Web of Science ®Google Scholar
• Yurek-George, A., Cecil, A. R. L., Mo, A. H. K., Wen, S., Rogers, H., Habens, F., … Ganesan, A. (2007). The first biologically active synthetic analogues of FK228 depsipeptide histone deacetylase inhibitor. Journal of Medicinal Chemistry, 50(23), 5720–5726. doi:10.1021/jm0703800
   PubMed Web of Science ®Google Scholar
• Zeng, X., Yin, B., Hu, Z., Liao, C., Liu, J., Li, S., … Jiang, S. (2010). Total synthesis and biological evaluation of largazole and derivatives with promising selectivity for cancers cells. Organic Letters, 12(6), 1368–1371. doi:10.1021/ol100308a
   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 and Dynamics, 36(8), 1966–1978. doi:10.1080/07391102.2017.1344568
   PubMed Web of Science ®Google Scholar