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Research Articles

Essential elements regulating HDAC8 inhibition: a classification based structural analysis and enzyme-inhibitor interaction study of hydroxamate based HDAC8 inhibitors

, ORCID Icon, ORCID Icon & ORCID Icon
Pages 5513-5525 | Received 17 Oct 2019, Accepted 06 Dec 2019, Published online: 23 Dec 2019

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
  • 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. doi:10.3892/or.2016.5280
  • Amin, S. A., Adhikari, N., & Jha, T. (2017a). 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
  • Amin, S. A., Adhikari, N., & Jha, T. (2017b). 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
  • Amin, S. A., Adhikari, N., & Jha, T. (2018a). Structure-activity relationships of HDAC8 inhibitors: Non-hydroxamates as anticancer agents. Pharmacological Research, 131, 128–142. doi:10.1016/j.phrs.2018.03.001
  • 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. doi:10.4155/fmc-2018-0005
  • Amin, S. A., Adhikari, N., & Jha, T. (2019). Development of decision trees to discriminate HDAC8 inhibitors and non-inhibitors using recursive partitioning. Journal of Biomolecular Structure and Dynamics, 1–8. In press. doi:10.1080/07391102.2019.1661876
  • 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. doi:10.1080/07391102.2018.1477625
  • Andrianov, V., Gailite, V., Lola, D., Loza, E., Semenikhina, V., Kalvinsh, I., … Sehested, M. (2009). Novel amide derivatives as inhibitors of histone deacetylase: Design, synthesis and SAR. European Journal of Medicinal Chemistry, 44(3), 1067–1085. doi:10.1016/j.ejmech.2008.06.020
  • Balasubramanian, S., Ramos, J., Luo, W., Sirisawad, M., Verner, E., & Buggy, J. J. (2008). A novel histone deacetylase 8 (HDAC8)-specific inhibitor PCI-34051 induces apoptosis in T-cell lymphomas. Leukemia, 22(5), 1026–1034. doi:10.1038/leu.2008.9
  • Banerjee, S., Adhikari, N., Amin, S. A., & Jha, T. (2019a). 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
  • Banerjee, S., Adhikari, N., Amin, S. A., & Jha, T. (2019b). Structural exploration of tetrahydroisoquinoline derivatives as HDAC8 inhibitors through multi-QSAR modeling study. Journal of Biomolecular Structure and Dynamics, 1–14. doi:10.1080/07391102.2019.1617782
  • Binding Data Base (Binding DB) Retrieved from http://www.bindingdb.org/
  • Box, G. E., & Tiao, C. C. (2011). Bayesian inference in statistical analysis. New York, NY: John Wiley & Sons.
  • Bressi, J. C., de Jong, R., Wu, Y., Jennings, A. J., Brown, J. W., O’Connell, S., … Gangloff, A. R. (2010). Benzimidazole and imidazole inhibitors of histone deacetylases: Synthesis and biological activity. Bioorganic & Medicinal Chemistry Letters, 20, 3138–3141. doi:10.1016/j.bmcl.2010.03.092
  • Cai, J., Wei, H., Hong, K. H., Wu, X., Cao, M., Zong, X., … Ji, M. (2015). Discovery and preliminary evaluation of 2-aminobenzamide and hydroxamate derivatives containing 1,2,4-oxadiazole moiety as potent histone deacetylase inhibitors. European Journal of Medicinal Chemistry, 96, 1–13. doi:10.1016/j.ejmech.2015.04.002
  • 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
  • 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. doi:10.1021/mp100465q
  • Chen, Q. W., Zhu, X. Y., Li, Y. Y., & Meng, Z. Q. (2014). Epigenetic regulation and cancer (review). Oncology Reports, 31(2), 523–532. doi:10.3892/or.2013.2913
  • Cramer, R. D. (2012). The inevitable QSAR renaissance. Journal of Computer-Aided Molecular Design, 26(1), 35–38. doi:10.1007/s10822-011-9495-0
  • David, R., & Mathew, H. (2010). Extended-connectivity fingerprints. Journal of Chemical Information and Modeling, 50, 742–754.
  • Discovery Studio 3.0 (DS 3.0). (2015). Accelrys Inc., San Diego, CA. Retrieved from http://www.accelrys.com
  • Ediriweera, M. K., Tennekoon, K. H., & Samarakoon, S. R. (2019). Emerging role of histone deacetylase inhibitors as anti-breast-cancer agents. Drug Discovery Today, 24(3), 685–702. doi:10.1016/j.drudis.2019.02.003
  • Extended Connectivity Fingerprint ECFP. Retrieved from https://docs.chemaxon.com/display/docs/Extended+Connectivity+Fingerprint+ECFP
  • Fawcett, T. (2006). An introduction to ROC analysis. Pattern Recognition Letters, 27(8), 861–874. doi:10.1016/j.patrec.2005.10.010
  • Gálvez-Llompart, M., Recio, M. C., & García-Domenech, R. (2011). Topological virtual screening: A way to find new compounds active in ulcerative colitis by inhibiting NF-kB. Molecular Diversity, 15(4), 917–926. doi:10.1007/s11030-011-9323-4
  • Glen, R. C., Bender, A., Arnby, C. H., Carlsson, L., Boyer, S., & Smith, J. (2006). Circular fingerprints: Flexible molecular descriptors with applications from physical chemistry to ADME. IDrugs, 9, 199–204.
  • Halder, A. K., Saha, A., & Jha, T. (2013). Exploring QSAR and pharmacophore mapping of structurally diverse selective matric metalloproteinase-2 inhibitors. Journal of Pharmacy and Pharmacology, 65(10), 1541–1554. doi:10.1111/jphp.12133
  • Heimburg, T., Chakrabarti, A., Lancelot, J., Marek, M., Melesina, J., Hauser, A. T., … Sippl, W. (2016). Structure-based design and synthesis of novel inhibitors targeting HDAC8 from schistosoma mansoni for the treatment of schistosomiasis. Journal of Medicinal Chemistry, 59(6), 2423–2435. doi:10.1021/acs.jmedchem.5b01478
  • Hu, Y., Lounkine, E., & Bajorath, J. (2009). Improving the search performance of extended connectivity fingerprints through activity-oriented feature filtering and application of a bit-density-dependent similarity function. ChemMedChem, 4(4), 540–548. doi:10.1002/cmdc.200800408
  • 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
  • Kar, S., & Roy, K. (2013). First report on predictive chemometric modeling, 3D-toxicophore mapping and in silico screening of in vitro basal cytotoxicity of diverse organic chemicals. Toxicology in Vitro, 27(2), 597–608.
  • Lambrinidis, G., & Tsantili-Kakoulidou, A. (2018). Challenges with multi-objective QSAR in drug discovery. Expert Opinion on Drug Discovery, 13(9), 851–859. doi:10.1080/17460441.2018.1496079
  • Lipinski, C. A., Lombardo, F., Dominy, B. W., & Feeney, P. J. (2001). Experimental and computational approaches to estimate solubility and permeability in drug discovery and development settings. Advanced Drug Delivery Reviews, 46(1-3), 3–26. doi:10.1016/j.addr.2012.09.019
  • Lo, Y. C., Rensi, S. E., Torng, W., & Altman, R. B. (2018). Machine learning in chemoinformatics and drug discovery. Drug Discovery Today, 23 (8), 1538–1546. doi:10.1016/j.drudis.2018.05.010
  • Marek, M., Shaik, T. B., Heimburg, T., Chakrabarti, A., Lancelot, J., Ramos-Morales, E., … Romier, C. (2018). Characterization of histone deacetylase 8 (HDAC8) selective inhibition reveals specific active site structural and functional determinants. Journal of Medicinal Chemistry, 61(22), 10000–10016. doi:10.1021/acs.jmedchem.8b01087
  • Marks, P. A., & Dokmanovic, M. (2005). Histone deacetylase inhibitors: Discovery and development as anticancer agents. Expert Opinion on Investigational Drugs, 14(12), 1497–1511. doi:10.1517/13543784.14.12.1497
  • Müller, M. M., & Muir, T. W. (2015). Histones: At the crossroads of peptide and protein chemistry. Chemical Reviews, 115(6), 2296–2349. doi:10.1021/cr5003529
  • New, M., Olzscha, H., & La Thangue, N. B. (2012). HDAC inhibitor-based therapies: Can we interpret the code? Molecular Oncology, 6(6), 637–656.
  • Polishchuk, P. (2017). Interpretation of quantitative structure-activity relationship models: Past, present, and future. Journal of Chemical Information and Modeling, 57(11), 2618–2639.
  • RCSB Protein Data Bank. Retrieved from www.rcsb.org/pdb/
  • Roche, J., & Bertrand, P. (2016). Inside HDACs with more selective HDAC inhibitors. European Journal of Medicinal Chemistry, 121, 451–483.
  • Rogers, D., Brown, R. D., & Hahn, M. (2005). Using extended-connectivity fingerprints with Laplacian-modified Bayesian analysis in high-throughput screening follow-up. Journal of Biomolecular Screening, 10(7), 682–686. doi:10.1177/1087057105281365
  • 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
  • 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
  • Suzuki, T., Muto, N., Bando, M., Itoh, Y., Masaki, A., Ri, M., … Miyata, N. (2014). Design, synthesis, and biological activity of NCC149 derivatives as histone deacetylase 8-selective inhibitors. ChemMedChem, 9(3), 657–664. doi:10.1002/cmdc.201300414
  • O’Boyle, N. M., & Sayle, R. A. (2016). Comparing structural fingerprints using a literature-based similarity benchmark. Journal of Cheminformatics, 8, 36.
  • Veber, D. F., Johnson, S. R., Cheng, H. Y., Smith, B. R., Ward, K. W., & Kopple, K. D. (2002). Molecular properties that influence the oral bioavailability of drug candidates. Journal of Medicinal Chemistry, 45(12), 2615–2623. doi:10.1021/jm020017n
  • Xia, X. Y., Maliski, E. G., Gallant, P., & Rogers, D. (2004). Classification of kinase inhibitors using a bayesian model. Journal of Medicinal Chemistry, 47(18), 4463–4470. doi:10.1021/jm0303195
  • You, J. S., & Jones, P. A. (2012). Cancer genetics and epigenetics: Two sides of the same coin? Cancer Cell, 22(1), 9–20. doi:10.1016/j.ccr.2012.06.008
  • Zhang, Y., Feng, J., Liu, C., Fang, H., & Xu, W. (2011). Design, synthesis and biological evaluation of tyrosine-based hydroxamic acid analogs as novel histone deacetylases (HDACs) inhibitors. Bioorganic & Medicinal Chemistry, 19(15), 4437–4444. doi:10.1016/j.bmc.2011.06.046

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