References
- Adhikari, N., Amin, S. A., Trivedi, P., Jha, T., & Ghosh, B. (2018). HDAC3 is a potential validated target for cancer: An overview on the benzamide-based selective HDAC3 inhibitors through comparative SAR/QSAR/QAAR approaches. European Journal of Medicinal Chemistry, 157, 1127–1142.
- Adhikari, N., Halder, A. K., Mallick, S., Saha, A., Saha, K. D., & Jha, T. (2016). Robust design of some selective matrix metalloproteinase-2 inhibitors over matrix metalloproteinase-9 through in silico/fragment-based lead identification and de novo lead modification: Syntheses and biological assays. Bioorganic & Medicinal Chemistry, 24(18), 4291–4309.
- Ahn, M. Y., & Yoon, J. H. (2017). Histone deacetylase 8 as a novel therapeutic target in oral squamous cell carcinoma. Oncology Reports, 37(1), 540–546.
- Amin, S. A., Adhikari, N., Jha, T., & Ghosh, B. (2019). Designing potential HDAC3 inhibitors to improve memory and learning. Journal of Biomolecular Structure and Dynamics, 37(8), 2133–2142.
- Amin, S. A., Adhikari, N., & Jha, T. (2018a). Structure-activity relationships of HDAC8 inhibitors: Non-hydroxamates as anticancer agents. Pharmacological Research, 131, 128–142.
- Amin, S. A., Adhikari, N., & Jha, T. (2018b). Diverse classes of HDAC8 inhibitors: In search of molecular fingerprints that regulate activity. Future Medicinal Chemistry, 10(13), 1589–1602.
- 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.
- 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.
- Bertrand, P., (2010). Inside HDAC with HDAC inhibitors. European Journal of Medicinal Chemistry, 45(6). 2095–2116.
- Binding database (DB). (2017). Binding Data Base (Binding DB) a tool available at http://www.bindingdb.org/.
- Biswas, S., & Rao, C. M. (2017). Epigenetics in cancer: Fundamentals and beyond. Pharmacology & Therapeutics, 173, 118–134.
- Bowman, G. D., & Poirier, M. G. (2015). Post-translational modifications of histones that influence nucleosome dynamics. Chemical Review, 115(6), 2274–2295.
- 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, 1609–1634. doi: 10.4155/fmc-2016-0117
- 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
- Chen, L., Li, Y., Zhao, Q., Peng, H., & Hou, T. (2011). ADME evaluation in drug discovery. 10. Predictions of P-glycoprotein inhibitors using recursive partitioning and Naive Bayesian classification techniques. Molecular Pharmaceutics, 8(3), 889–900.
- Chen, Q. W., Zhu, X. Y., Li, Y. Y., & Meng, Z. Q. (2014). Epigenetic regulation and cancer. Oncology Reports, 31(2), 523–532.
- David, R., & Mathew, H. (2010). Extended-connectivity fingerprints. Journal of Chemical Information and Modeling, 50, 742–754.
- Accelrys Inc., San Diego, USA. 2015. Discovery Studio 3.0 (DS 3.0), software. Retrieved from http://www.accelrys.com
- Haberland, M., Montgomery, R. L., & Olson, E. N. (2009). The many roles of histone deacetylases in development and physiology: Implications for disease and therapy. Nature Reviews Genetics, 10(1), 32–42.
- Halder, A. K., Mallick, S., Shikha, D., Saha, A., Saha, K. D., & Jha, T. (2015). Design of dual MMP-2/HDAC-8 inhibitors by pharmacophore mapping, molecular docking, synthesis and biological activity. RSC Advances, 5(88), 72373–72386.
- Halder, A. K., Saha, A., & Jha, T. (2013). Exploring QSAR and pharmacophore mapping of structurally diverse selective matrix metalloproteinase-2 inhibitors. Journal of Pharmacy & Pharmacology, 65(10), 1541–1554.
- Heimburg, T., Kolbinger, F. R., Zeyen, P., Ghazy, E., Herp, D., Schmidtkunz, K., … Sippl, W. (2017). Structure-based design and biological characterization of selective histone deacetylase 8 (HDAC8) inhibitors with anti-neuroblastoma activity. Journal of Medicinal Chemistry, 60(24), 10188–10204. doi: 10.1021/acs.jmedchem.7b01447
- 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, 1–18. doi: 10.1080/07391102.2019.1567388
- Lehmann, M., Hoffmann, M. J., Koch, A., Ulrich, S. M., Schulz, W. A., & Niegisch, G. (2014). Histone deacetylase 8 is deregulated in urothelial cancer but not a target for efficient treatment. Journal of Experimental & Clinical Cancer Research, 33, 59.
- Lopez, G., Bill, K. L. J., Bid, H. K., Braggio, D., Constantino, D., Prudner, B., … Pollock, R. E. (2015). HDAC8, A potential therapeutic target for the treatment of malignant peripheral nerve sheath tumors (MPNST). PLoS One, 10(7), e0133302. doi: 10.1371/journal.pone.0133302
- Marks, P. A., & Dokmanovic, M. (2005). Histone deacetylase inhibitors: Discovery and development as anticancer agents. Expert Opinion on Investigational Drugs, 14(12), 1497–1511.
- Müller, M. M., & Muir, T. W. (2015). Histones: At the crossroads of peptide and protein chemistry. Chemical Review, 115(6), 2296–2349.
- O’Boyle, N. M., & Sayle, R. A. (2016). Comparing structural fingerprints using a literature‐based similarity benchmark. Journal of Cheminformatics, 8, 36.
- Oehme, I., Deubzer, H. E., Wegener, D., Pickert, D., Linke, J. P., Hero, B., Kopp-Schneider, A., … Witt, O. (2009). Histone deacetylase 8 in neuroblastoma tumorigenesis. Clinical Cancer Research, 15, 91–99. doi: 10.1158/1078-0432.CCR-08-0684
- R, M., P, H. A., & Mahadevan, V. (2018). HDAC inhibitors show differential epigenetic regulation and cell survival strategies on p53 mutant colon cancer cells. Journal of Biomolecular Structure &Amp; Dynamics, 36(4), 938–955. doi: 10.1080/07391102.2017.1302820
- Sastry, M., Lowrie, J. F., Dixon, S. L., & Sherman, W. (2010). Large-scale systematic analysis of 2D fingerprint methods and parameters to improve virtual screening enrichments. Journal of Chemical Information and Modeling, 50(5), 771–784.
- 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, 1–20. doi: 10.1080/07391102.2018.1557560
- 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.
- Song, S., Wang, Y., Xu, P., Yang, R., Ma, Z., Liang, S., & Zhang, G. (2015). The inhibition of histone deacetylase 8 suppresses proliferation and inhibits apoptosis in gastric adenocarcinoma. International Journal of Oncology, 47(5), 1819–1828. doi: 10.3892/ijo.2015.3182
- Tang, W., Luo, T., Greenberg, E. F., Bradner, J. E., & Schreiber, S. L. (2011). Discovery of histone deacetylase 8 selective inhibitors. Bioorganic & Medicinal Chemistry Letters, 21(9), 2601–2605.
- Trivedi, P., Adhikari, N., Amin, S. A., Jha, T., & Ghosh, B. (2018). Design, synthesis and biological screening of 2-aminobenzamides as selective HDAC3 inhibitors with promising anticancer effects. European Journal of Pharmaceutical Sciences : Official Journal of the European Federation for Pharmaceutical Sciences, 124, 165–181. doi: 10.1016/j.ejps.2018.08.030
- Uba, A. I., & Yelekçi, K. (2018). 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, 36(12), 3231–3245.
- 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, 37, 3627–3636.
- 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.
- Xu, W. S., Parmigiani, R. B., & Marks, P. A. (2007). Histone deacetylase inhibitors: Molecular mechanisms of action. Oncogene, 26(37), 5541–5552.
- Yuan, Y., Hu, Z., Bao, M., Sun, R., Long, X., Long, L., … Bao, J. (2019). 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 &Amp; Dynamics, 37(15), 4092–4103. doi: 10.1080/07391102.2018.1541141
- 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, 1966–1978.