Structural exploration of tetrahydroisoquinoline derivatives as HDAC8 inhibitors through multi-QSAR modeling study

References

• Amin, S. A., Adhikari, N., Baidya, S. K., Gayen, S., & Jha, T. (2019a). Structural refinement and prediction of potential CCR2 antagonists through validated multi-QSAR modeling studies. Journal of Biomolecular Structure and Dynamics, 37(1), 75–94.
   PubMed Web of Science ®Google Scholar
• Amin, S. A., Adhikari, N., Gayen, S., & Jha, T. (2017c). First report on the structural exploration and prediction of new BPTES analogs as glutaminase inhibitors. Journal of Molecular Structure, 1143, 49–64. doi: 10.1016/j.molstruc.2017.04.020
   Web of Science ®Google Scholar
• 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.
   PubMed Web of Science ®Google Scholar
• 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.
   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.
   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, 131, 128–142.
   PubMed Web of Science ®Google Scholar
• Amin, S. A., Adhikari, N., Jha, T., & Ghosh, B. (2019b). Designing potential HDAC3 inhibitors to improve memory and learning. Journal of Biomolecular Structure and Dynamics, 37(8), 2133–2142.
   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.
   PubMed Web of Science ®Google Scholar
• Bertrand, P., (2010). Inside HDAC with HDAC inhibitors. European Journal of Medicinal Chemistry, 45(6), 2095–2116.
   PubMed 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.
   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.
   PubMed Web of Science ®Google Scholar
• Chem 3D Pro Version 5.0 and Chem Draw Ultra Version 5.0. (2015). [Software programs]. USA: Cambridge Soft Corporation.
   Google Scholar
• Dewaker, V., Srivastava, P. N., Verma, S., & Prabhakar, Y. S. (2019). Molecular dynamics study of HDAC8-largazole analogues co-crystals for designing potential anticancer compounds. Journal of Biomolecular Structure and Dynamics, 1–59 (published online). [ doi: 10.1080/07391102.2019.1598497
   Web of Science ®Google Scholar
• Discovery Studio 3.0 (2011). San Diego, CA: Accelrys Software Inc.
   Google Scholar
• Durst, K. L., Lutterbach, B., Kummalue, T., Friedman, A. D., & Hiebert, S. W. (2003). The inv (16) fusion protein associates with corepressors via a smooth muscle myosin heavy-chain domain. Molecular and Cellular Biology, 23(2), 607–619.
   PubMed Web of Science ®Google Scholar
• Fenichel, M. P. (2015). FDA approves new agent for multiple myeloma. Journal of the National Cancer Institute, 107, 6–7.
   Google Scholar
• Gaikwad, R., Amin, S. A., Adhikari, N., Ghorai, S., Jha, T., & Gayen, S., (2017). Identification of molecular fingerprints of phenylindole derivatives as cytotoxic agents: A multi-QSAR approach. Structural Chemistry, 29(4), 1095–1107.
   Web of Science ®Google Scholar
• Gasteiger, J., & Marsili, M. (1980). Iterative partial equalization of orbital electronegativity – a rapid access to atomic charges. Tetrahedron, 36(22), 3219–3228.
   Web of Science ®Google Scholar
• Golbraikh, A., & Tropsha, A. (2002). Beware of q2!. Journal of Molecular Graphics and Modelling, 20(4), 269–276.
   PubMed Web of Science ®Google Scholar
• Gregoretti, I. V., Lee, Y. M., & Goodson, H. V. (2004). Molecular evolution of the histone deacetylase family: Functional implications of phylogenetic analysis. Journal of Molecular Biology, 338(1), 17–31.
   PubMed Web of Science ®Google Scholar
• Higuchi, T., Nakayama, T., Arao, T., Nishio, K., & Yoshie, O. (2013). SOX4 is a direct target gene of FRA-2 and induces expression of HDAC8 in adult T-cell leukemia/lymphoma. Blood, 121(18), 3640–3649.
   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, 1–22 (published online). doi: 10.1080/07391102.2019.1567388
   Web of Science ®Google Scholar
• Klon, A. E., Lowrie, J. F., & Diller, D. J. (2006). Improved naïve Bayesian modeling of numerical data for absorption distribution, metabolism and excretion (ADME) property prediction. Journal of Chemical Information and Modeling, 46(5), 1945–1956.
   PubMed Web of Science ®Google Scholar
• Lutterbach, B., & Hiebert, S. W. (2000). Role of the transcription factor AML-1 in acute leukemia and hematopoietic differentiation. Gene, 245(2), 223–235.
   PubMed Web of Science ®Google Scholar
• Mandi, P., Nantasenamat, C., Srungboonmee, K., Isarankura-Na-Ayudhya, C., & Prachayasittikul, V. (2012). QSAR study of anti-prion activity of 2-aminothiazoles. EXCLI Journal, 11, 453–467.
   PubMed Web of Science ®Google Scholar
• Mann, B. S., Johnson, J. R., Cohen, M. H., Justice, R., & Pazdur, R. (2007). FDA approval summary: Vorinostat for treatment of advanced primary cutaneous t-cell lymphoma. The Oncologist, 12(10), 1247–1252.
   PubMed Web of Science ®Google Scholar
• Marek, M., Kannan, S., Hauser, A.-T., Mourão, M. M., Caby, S., Cura, V., … Romier, C. (2013). Structural basis for the inhibition of histone deacetylase 8 (HDAC8), a key epigenetic player in the blood fluke Schistosoma mansoni. PLoS Pathogens, 9(9), e1003645. doi: 10.1371/journal.ppat.1003645
   PubMed Web of Science ®Google Scholar
• Matter, H., Schudok, M., Schwab, W., Thorwart, W., Barbier, D., Billen, G., … Wollmann, T. (2002). Tetrahydroisoquinoline-3-carboxylate based matrix-metalloproteinase inhibitors: Design, synthesis and structure–activity relationship. Bioorganic Medicinal Chemistry, 10(11), 3529–3544. doi: 10.1016/S0968-0896(02)00215-8
   PubMed Web of Science ®Google Scholar
• Mottamal, M., Zheng, S., Huang, T. L., & Wang, G. (2015). Histone deacetylase inhibitors in clinical studies as templates for new anticancer agents. Molecules, 20(3), 3898–3941.
   PubMed Web of Science ®Google Scholar
• Nakagawa, M., Oda, Y., Eguchi, T., Aishima, S., Yao, T., Hosoi, F., … Tsuneyoshi, M. (2007). Expression profile of class I histone deacetylases in human cancer tissues. Oncology Reports, 18, 769–774.
   PubMed Web of Science ®Google Scholar
• Novotny-Diermayr, V., Sangthongpitag, K., Hu, C. Y., Wu, X., Sausgruber, N., Yeo, P., … Wood, J. M. (2010). SB939, a novel potent and orally active histone deacetylase inhibitor with high tumor exposure and efficacy in mouse models of colorectal cancer. Molecular Cancer Therapeutics, 9(3), 642–652. doi: 10.1158/1535-7163.MCT-09-0689
   PubMed Web of Science ®Google Scholar
• Oehme, I., Deubzer, H. E., Wegener, D., Pickert, D., Linke, J.-P., Hero, B., … Witt, O. (2009). Histone deacetylase 8 in neuroblastoma tumorigenesis. Clinical Cancer Research, 15(1), 91–99. doi: 10.1158/1078-0432.CCR-08-0684
   PubMed Web of Science ®Google Scholar
• Park, S. Y., Jun, J. A., Jeong, K. J., Heo, H. J., Sohn, J. S., Lee, H. Y., … Kang, J. (2011). Histone deacetylases 1, 6 and 8 are critical for invasion in breast cancer. Oncology Reports, 25, 1677–1681.
   PubMed Web of Science ®Google Scholar
• Qiao, Z., Ren, S., Li, W., Wang, X., He, M., Guo, Y., … Yu, Q. (2013). Chidamide, a novel histone deacetylase inhibitor, synergistically enhances gemcitabine cytotoxicity in pancreatic cancer cells. Biochemical and Biophysical Research Communications, 434(1), 95–101. doi: 10.1016/j.bbrc.2013.03.059
   PubMed Web of Science ®Google Scholar
• Seto, E., & Yoshida, M. (2014). Erasers of histone acetylation: The histone deacetylase enzymes. Cold Spring Harbor in Perspective Biology, 6(4), a018713.
   PubMed Web of Science ®Google Scholar
• SYBYL-X 2.0 (2015). St. Louis, MO: Certara USA, Inc. Software available at http://www.certara.com.
   Google Scholar
• Taha, T. Y., Aboukhatwa, S. M., Knopp, R. C., Ikegaki, N., Abdelkarim, H., Neerasa, J., … Petukhov, P. A. (2017). Design, synthesis, and biological evaluation of tetrahydroisoquinoline-based histone deacetylase 8 selective inhibitors. ACS Medicinal Chemistry Letters, 8(8), 824–829. doi: 10.1021/acsmedchemlett.7b00126
   PubMed Web of Science ®Google Scholar
• Vyas, V. K., Ghate, M., & Gupta, N. (2017). 3D QSAR and HQSAR analysis of protein kinase B (PKB/Akt) inhibitors using various alignment methods. Arabian Journal of Chemistry, 10, S2182–S2195.
   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.
   PubMed Web of Science ®Google Scholar
• Wu, J., Du, C., Lv, Z., Ding, C., Cheng, J., Xie, H., … Zheng, S. (2013). The up-regulation of histone deacetylase 8 promotes proliferation and inhibits apoptosis in hepatocellular carcinoma. Digestive Diseases and Sciences, 58(12), 3545–3553.
   PubMed Web of Science ®Google Scholar
• Yamauchi, Y., Boukari, H., Banerjee, I., Sbalzarini, I. F., Horvath, P., & Helenius, A. (2011). Histone deacetylase 8 is required for centrosome cohesion and influenza A virus entry. PLoS Pathogens, 7(10), e1002316.
   PubMed Web of Science ®Google Scholar
• Yap, C. W. (2011). PaDELe Descriptor: An open source software to calculate molecular descriptors and fingerprints. Journal of Computational. Chemistry, 32(7), 1466–1474.
   PubMed Web of Science ®Google Scholar
• Yu, S., Yuan, J., Shi, J., Ruan, X., Zhang, T., Wang, Y., & Du, Y. (2015). HQSAR and topomer CoMFA for predicting melanocortin-4 receptor binding affinities of trans-4-(4-chlorophenyl) pyrrolidine-3-carboxamides. Chemometrics and Intelligent Laboratory Systems, 146, 34–41.
   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 (published online). doi: 10.1080/07391102.2018.1541141
   PubMed Web of Science ®Google Scholar
• Zhang, Y., Fang, H., Feng, J., Jia, Y., Wang, X., & Xu, W. (2011). Discovery of a tetrahydroisoquinoline-based hydroxamic acid derivative (ZYJ-34c) as histone deacetylase inhibitor with potent oral antitumor activities. Journal of Medicinal Chemistry, 54(15), 5532–5539.
   PubMed Web of Science ®Google Scholar
• Zhang, Y., Feng, J., Jia, Y., Wang, X., Zhang, L., Liu, C., … Xu, W. (2011). Development of tetrahydroisoquinoline-based hydroxamic acid derivatives: potent histone deacetylase inhibitors with marked in vitro and in vivo antitumor activities. Journal of Medicinal Chemistry, 54(8), 2823–2838.
   PubMed Web of Science ®Google Scholar
• Zhang, Y., Feng, J., Liu, C., Zhang, L., Jiao, J., Fang, H., … Xu, W. (2010). Design, synthesis and preliminary activity assay of 1, 2, 3, 4-tetrahydroisoquinoline-3-carboxylic acid derivatives as novel histone deacetylases (HDACs) inhibitors. Bioorganic Medicinal Chemistry, 18(5), 1761–1772. doi: 10.1016/j.bmc.2010.01.060
   PubMed Web of Science ®Google Scholar
• Zhao, X., Chen, M., Huang, B., Ji, H., & Yuan, M. (2011). Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) studies on α 1A-adrenergic receptor antagonists based on pharmacophore molecular alignment. International Journal of Molecular Sciences, 12(10), 7022–7037.
   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.
   PubMed Web of Science ®Google Scholar