343
Views
20
CrossRef citations to date
0
Altmetric
Research Articles

Identification of high-affinity inhibitors of pyruvate dehydrogenase kinase-3: towards therapeutic management of cancer

ORCID Icon, , , , , & ORCID Icon show all
Pages 586-594 | Received 22 Dec 2019, Accepted 30 Dec 2019, Published online: 14 Jan 2020

References

  • Ali, S., Khan, F. I., Mohammad, T., Lan, D., Hassan, M. I., & Wang, Y. (2019). Identification and Evaluation of Inhibitors of Lipase from Malassezia restricta using Virtual High-Throughput Screening and Molecular Dynamics Studies. International Journal of Molecular Sciences, 20(884), 1–19.
  • Biovia, D. S. (2015). Discovery studio modeling environment. San Diego: Dassault Systèmes.
  • Cui, L., Cheng, Z., Liu, Y., Dai, Y., Pang, Y., Jiao, Y., … Shi, J. (2018). Overexpression of PDK2 and PDK3 reflects poor prognosis in acute myeloid leukemia. Cancer Gene Therapy, 1. doi:10.1038/s41417-018-0071-9
  • Dahiya, R., Mohammad, T., Roy, S., Anwar, S., Gupta, P., Haque, A., … Hassan, M. I. (2019). Investigation of inhibitory potential of quercetin to the pyruvate dehydrogenase kinase 3: Towards implications in anticancer therapy. International Journal of Biological Macromolecules, 136, 1076–1085. doi:10.1016/j.ijbiomac.2019.06.158
  • Dahiya, R., Mohammad, T., Roy, S., Anwar, S., Gupta, P., ... Hassan, M. I. (2019). Investigation of inhibitory potential of quercetin to the pyruvate dehydrogenase kinase 3: Towards implications in anticancer therapy. International Journal of Biological Macromolecules, 136, 1076–1085. doi:10.1016/j.ijbiomac.2019.06.158
  • Daina, A., Michielin, O., & Zoete, V. (2017). SwissADME: A free web tool to evaluate pharmacokinetics, drug-likeness and medicinal chemistry friendliness of small molecules. Scientific Reports, 7(1), 42717. doi:10.1038/srep42717
  • Devika, N. T., Amresh, P., Hassan, M. I., & Ali, B. M. (2014). Molecular modeling and simulation of the human eNOS reductase domain, an enzyme involved in the release of vascular nitric oxide. Journal of Molecular Modeling, 20, 2470. doi:10.1007/s00894-014-2470-7
  • Fatima, S., Mohammad, T., Jairajpuri, D. S., Rehman, M. T., Hussain, A., Samim, M., … Hassan, M. I. (2019). Identification and evaluation of glutathione conjugate gamma-l-glutamyl-l-cysteine for improved drug delivery to the brain. Journal of Biomolecular Structure and Dynamics, 1–11.
  • Fischer, E. H. (1993). Protein phosphorylation and cellular regulation II (Nobel lecture). Angewandte Chemie International Edition in English, 32, 1130–1137. doi:10.1002/anie.199311301
  • Gudi, R., Melissa, M. B.-K., Kedishvili, N. Y., Zhao, Y., & Popov, K. M. (1995). Diversity of the pyruvate dehydrogenase kinase gene family in humans. Journal of Biological Chemistry, 270, 28989–28994. doi:10.1074/jbc.270.48.28989
  • Gulzar, M., Ali, S., Khan, F. I., Khan, P., Taneja, P., & Hassan, M. I. (2019). Binding mechanism of caffeic acid and simvastatin to the integrin linked kinase for therapeutic implications: A comparative docking and MD simulation studies. Journal of Biomolecular Structure and Dynamics, 37, 4327–4337. doi:10.1080/07391102.2018.1546621
  • Gulzar, M., Syed, S. B., Khan, F. I., Khan, P., Ali, S., Hasan, G. M., … Hassan, M. I. (2019). Elucidation of interaction mechanism of ellagic acid to the integrin linked kinase. International Journal of Biological Macromolecules, 122, 1297–1304. doi:10.1016/j.ijbiomac.2018.09.089
  • Gupta, P., Mohammad, T., Dahiya, R., Roy, S., Noman, O. M. A., Alajmi, M. F., … Hassan, M. I. (2019). Evaluation of binding and inhibition mechanism of dietary phytochemicals with sphingosine kinase 1: Towards targeted anticancer therapy. Scientific Reports, 9(1), 1–15. doi:10.1038/s41598-019-55199-3
  • Gupta, P., Mohammad, T., Khan, P., Alajmi, M. F., Hussain, A., Rehman, M. T., & Hassan, M. I. (2019). Evaluation of ellagic acid as an inhibitor of sphingosine kinase 1: A targeted approach towards anticancer therapy. Biomedicine & Pharmacotherapy, 118, 109245. doi:10.1016/j.biopha.2019.109245
  • Hubbard, R. E., & Kamran Haider, M. (2001). Hydrogen bonds in proteins: Role and strength. Chichester: John Wiley & Sons, Ltd. doi:10.1002/9780470015902.a0003011.pub2
  • Jacob, R. B., Andersen, T., & McDougal, O. M. (2012). Accessible high-throughput virtual screening molecular docking software for students and educators. PLoS Computational Biology, 8(5), e1002499. doi:10.1371/journal.pcbi.1002499
  • Jeoung, N. H. (2015). Pyruvate dehydrogenase kinases: Therapeutic targets for diabetes and cancers. Diabetes & Metabolism Journal, 39, 188–197. doi:10.4093/dmj.2015.39.3.188
  • Kato, M., Chuang, J. L., Tso, S. C., Wynn, R. M., & Chuang, D. T. (2005). Crystal structure of pyruvate dehydrogenase kinase 3 bound to lipoyl domain 2 of human pyruvate dehydrogenase complex. The EMBO Journal, 24, 1763–1774. doi:10.1038/sj.emboj.7600663
  • Khan, F. I., Wei, D. Q., Gu, K. R., Hassan, M. I., & Tabrez, S. (2016). Current updates on computer aided protein modeling and designing. International Journal of Biological Macromolecules, 85, 48–62. doi:10.1016/j.ijbiomac.2015.12.072
  • Khan, P., Queen, A., Mohammad, T., Smita, Khan, N. S., Hafeez, Z. B., … Ali, S. (2019). Identification of alpha-mangostin as a potential inhibitor of microtubule affinity regulating kinase 4. Journal of Natural Products, 82, 2252–2261. doi:10.1021/acs.jnatprod.9b00372
  • Khan, P., Rahman, S., Queen, A., Manzoor, S., Naz, F., Hasan, G. M., … Hassan, M. I. (2017). Elucidation of dietary polyphenolics as potential inhibitor of microtubule affinity regulating kinase 4: In silico and in vitro studies. Scientific Reports, 7(1), 9470. doi:10.1038/s41598-017-09941-4
  • Korotchkina, L. G., Sidhu, S., & Patel, M. S. (2006). Characterization of testis-specific isoenzyme of human pyruvate dehydrogenase. Journal of Biological Chemistry, 281, 9688–9696. doi:10.1074/jbc.M511481200
  • Kuzmanic, A., & Zagrovic, B. (2010). Determination of ensemble-average pairwise root mean-square deviation from experimental B-factors. Biophysical Journal, 98, 861–871. doi:10.1016/j.bpj.2009.11.011
  • 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. doi:10.1016/S1056-8719(00)00107-6
  • Lu, C.-W., Lin, S.-C., Chen, K.-F., Lai, Y.-Y., & Tsai, S.-J. (2008). Induction of pyruvate dehydrogenase kinase-3 by hypoxia-inducible factor-1 promotes metabolic switch and drug resistance. Journal of Biological Chemistry, 283, 28106–28114. doi:10.1074/jbc.M803508200
  • Lu, C.-W., Lin, S.-C., Chien, C.-W., Lin, S.-C., Lee, C.-T., Lin, B.-W., … Tsai, S.-J. (2011). Overexpression of pyruvate dehydrogenase kinase 3 increases drug resistance and early recurrence in colon cancer. The American Journal of Pathology, 179, 1405–1414. doi:10.1016/j.ajpath.2011.05.050
  • Malumbres, M., & Barbacid, M. (2007). Cell cycle kinases in cancer. Current Opinion in Genetics & Development, 17, 60–65. doi:10.1016/j.gde.2006.12.008
  • Mazola, Y., Guirola, O., Palomares, S., Chinea, G., Menendez, C., Hernandez, L., & Musacchio, A. (2015). A comparative molecular dynamics study of thermophilic and mesophilic beta-fructosidase enzymes. Journal of Molecular Modeling, 21, 2772. doi:10.1007/s00894-015-2772-4
  • Mohammad, T., Batra, S., Dahiya, R., Baig, M. H., Rather, I. A., Dong, J. J., & Hassan, I. (2019). Identification of high-affinity inhibitors of cyclin-dependent kinase 2 towards anticancer therapy. Molecules, 24, 4589. doi:10.3390/molecules24244589
  • Mohammad, T., Khan, F. I., Lobb, K. A., Islam, A., Ahmad, F., & Hassan, M. I. (2019). Identification and evaluation of bioactive natural products as potential inhibitors of human microtubule affinity-regulating kinase 4 (MARK4). Journal of Biomolecular Structure and Dynamics, 37, 1813–1829. doi:10.1080/07391102.2018.1468282
  • Naqvi, A. A. T., Jairajpuri, D. S., Noman, O. M. A., Hussain, A., Islam, A., Ahmad, F., … Hassan, M. I. (2019). Evaluation of pyrazolopyrimidine derivatives as microtubule affinity regulating kinase 4 inhibitors: Towards therapeutic management of Alzheimer's disease. Journal of Biomolecular Structure and Dynamics, 1–16.
  • Naqvi, A. A. T., Mohammad, T., Hasan, G. M., & Hassan, M. I. (2018). Advancements in docking and molecular dynamics simulations towards ligand-receptor interactions and structure-function relationships. Current Topics in Medicinal Chemistry, 18, 1755–1768. doi:10.2174/1568026618666181025114157
  • Naz, F., Khan, F. I., Mohammad, T., Khan, P., Manzoor, S., Hasan, G. M., … Hassan, M. I. (2018). Investigation of molecular mechanism of recognition between citral and MARK4: A newer therapeutic approach to attenuate cancer cell progression. International Journal of Biological Macromolecules, 107, 2580–2589. doi:10.1016/j.ijbiomac.2017.10.143
  • Naz, H., Khan, P., Tarique, M., Rahman, S., Meena, A., Ahamad, S., … Hassan, M. I. (2017). Binding studies and biological evaluation of beta-carotene as a potential inhibitor of human calcium/calmodulin-dependent protein kinase IV. International Journal of Biological Macromolecules, 96, 161–170. doi:10.1016/j.ijbiomac.2016.12.024
  • Naz, H., Tarique, M., Khan, P., Luqman, S., Ahamad, S., Islam, A., … Hassan, M. I. (2018). Evidence of vanillin binding to CAMKIV explains the anti-cancer mechanism in human hepatic carcinoma and neuroblastoma cells. Molecular and Cellular Biochemistry, 438(1–2), 35–45. doi:10.1007/s11010-017-3111-0
  • Saunier, E., Benelli, C., & Bortoli, S. (2016). The pyruvate dehydrogenase complex in cancer: An old metabolic gatekeeper regulated by new pathways and pharmacological agents. International Journal of Cancer, 138, 809–817. doi:10.1002/ijc.29564
  • Shamsi, A., Mohammad, T., Khan, M. S., Shahwan, M., Husain, F. M., Rehman, M. T., … Islam, A. (2019). Unraveling binding mechanism of Alzheimer's drug rivastigmine tartrate with human transferrin: Molecular docking and multi-spectroscopic approach towards neurodegenerative diseases. Biomolecules, 9, 495. doi:10.3390/biom9090495
  • Trott, O., & Olson, A. J. (2010). AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 31, 455–461. doi:10.1002/jcc.21334
  • Turner, P. (2005). XMGRACE, 5.1. Center for Coastal and Land-Margin Research. Beaverton, OR: Oregon Graduate Institute of Science and Technology.
  • Zhang, L., Ai, H., Chen, W., Yin, Z., Hu, H., Zhu, J., … Liu, H. (2017). CarcinoPred-EL: Novel models for predicting the carcinogenicity of chemicals using molecular fingerprints and ensemble learning methods. Scientific Reports, 7(1), 2118. doi:10.1038/s41598-017-02365-0
  • Zhang, W., Zhang, S.-L., Hu, X., & Tam, K. Y. (2015). Targeting tumor metabolism for cancer treatment: Is pyruvate dehydrogenase kinases (PDKs) a viable anticancer target? International Journal of Biological Sciences, 11, 1390–1400. doi:10.7150/ijbs.13325

Reprints and Corporate Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

To request a reprint or corporate permissions for this article, please click on the relevant link below:

Academic Permissions

Please note: Selecting permissions does not provide access to the full text of the article, please see our help page How do I view content?

Obtain permissions instantly via Rightslink by clicking on the button below:

If you are unable to obtain permissions via Rightslink, please complete and submit this Permissions form. For more information, please visit our Permissions help page.