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Research Articles

Amygdalin as multi-target anticancer drug against targets of cell division cycle: double docking and molecular dynamics simulation

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Pages 1965-1974 | Received 30 Jan 2020, Accepted 06 Mar 2020, Published online: 24 Mar 2020

References

  • Abraham, M. J., Murtola, T., Schulz, R., Pall, S., Smith, J. C., Hess, B., & Lindahl, E. (2015). GROMACS: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX, 1-2, 19–25. 10.1016/j.softx.2015.06.001
  • Al-Khafaji, K., & Taskin Tok, T. (2020). Understanding the mechanism of Amygdalin’s multifunctional anti-cancer action using computational approach. Journal of Biomolecular Structure and Dynamics, 1–14. 10.1080/07391102.2020.1736159
  • Amadei, A., Linssen, A. B., & Berendsen, H. J. (1993). Essential dynamics of proteins. Proteins: Structure, Function, and Genetics, 17(4), 412–425. 10.1002/prot.340170408
  • Barford, D. (2011). Structural insights into anaphase-promoting complex function and mechanism. Philosophical Transactions of the Royal Society B: Biological Sciences, 366(1584), 3605–3624. 10.1098/rstb.2011.0069
  • Bhatnagar, A., Mittal, S., & Garg, A. (2017). Laetrile: A wonder drug or farce. International Journal of Applied Dental Sciences 3(3), 42–45.
  • Biovia D. S. (2016). Dassault Systèmes BIOVIA, Discovery Studio, 2019, San Diego: Dassault Systèmes. Retrieved from https://www.3dsbiovia.com/about/citations-references/
  • Bjelkmar, P., Larsson, P., Cuendet, M. A., Hess, B., & Lindahl, E. (2010). Implementation of the CHARMM force field in GROMACS: Analysis of protein stability effects from correction maps, virtual interaction sites, and water models. Journal of Chemical Theory and Computation, 6(2), 459–466. 10.1021/ct900549r
  • Brown, N. R., Korolchuk, S., Martin, M. P., Stanley, W. A., Moukhametzianov, R., Noble, M. E., & Endicott, J. A. (2015). CDK1 structures reveal conserved and unique features of the essential cell cycle CDK. Nature Communications, 6(1), 6769. 10.1038/ncomms7769
  • Bruyère, C., & Meijer, L. (2013). Targeting cyclin-dependent kinases in anti-neoplastic therapy. Current Opinion in Cell Biology, 25(6), 772–779. 10.1016/j.ceb.2013.08.004
  • Chashoo, G., & Saxena, A. (2014). Targetting Cdks in cancer: An overview and new insights. Journal of Cancer Science and Therapy, 6(12), 488–496.
  • Clute, P., & Pines, J. (1999). Temporal and spatial control of cyclin B1 destruction in metaphase. Nature Cell Biology, 1(2), 82–87. 10.1038/10049
  • Cohen, P., & Alessi, D. R. (2013). Kinase drug discovery–what’s next in the field? ACS Chemical Biology, 8(1), 96–104. 10.1021/cb300610s
  • Coxon, C. R., Anscombe, E., Harnor, S. J., Martin, M. P., Carbain, B., Golding, B. T., Hardcastle, I. R., Harlow, L. K., Korolchuk, S., Matheson, C. J., Newell, D. R., Noble, M. E. M., Sivaprakasam, M., Tudhope, S. J., Turner, D. M., Wang, L. Z., Wedge, S. R., Wong, C., Griffin, R. J., Endicott, J. A., & Cano, C. (2017). Cyclin-dependent kinase (CDK) inhibitors: Structure–activity relationships and insights into the CDK-2 selectivity of 6-substituted 2-arylaminopurines. Journal of Medicinal Chemistry, 60(5), 1746–1767. 10.1021/acs.jmedchem.6b01254
  • Davies, T. G., Pratt, D. J., Endicott, J. A., Johnson, L. N., & Noble, M. E. (2002). Structure-based design of cyclin-dependent kinase inhibitors. Pharmacology & Therapeutics, 93(2-3), 125–133. 10.1016/S0163-7258(02)00182-1
  • Dickson, M. A. (2014). Molecular pathways: CDK4 inhibitors for cancer therapy. Clinical Cancer Research, 20(13), 3379–3383. 10.1158/1078-0432.CCR-13-1551
  • Dong, K., Yang, X., Zhao, T., & Zhu, X. (2017). An insight into the inhibitory selectivity of 4-(Pyrazol-4-yl)-pyrimidines to CDK4 over CDK2. Molecular Simulation, 43(8), 599–609. 10.1080/08927022.2017.1279283
  • Fry, D. W., Harvey, P. J., Keller, P. R., Elliott, W. L., Meade, M., Trachet, E., Albassam, M., Zheng, X., Leopold, W. R., Pryer, N. K., & Toogood, P. L. (2004). Specific inhibition of cyclin-dependent kinase 4/6 by PD 0332991 and associated antitumor activity in human tumor xenografts. Molecular Cancer Therapeutics, 3(11), 1427–1438.
  • Halenar, M., Medvedova, M., Maruniakova, N., & Kolesarova, A. (2013). Amygdalin and its effects on animal cells. Journal of Microbiology, Biotechnology and Food Sciences, 2, 1414–1423.
  • Hall, M., & Peters, G. (1996). Genetic alterations of cyclins, cyclin-dependent kinases, and Cdk inhibitors in human cancer. In George F. Vande Woude and George Klein (Eds.), Advances in cancer research (Vol. 68, pp. 67–108). Elsevier.
  • Holt, L. J., Tuch, B. B., Villén, J., Johnson, A. D., Gygi, S. P., & Morgan, D. O. (2009). Global analysis of Cdk1 substrate phosphorylation sites provides insights into evolution. Science, 325(5948), 1682–1686. 10.1126/science.1172867
  • Jaswal, V., Palanivelu, J., & C, R. (2018). Effects of the Gut microbiota on Amygdalin and its use as an anti-cancer therapy: Substantial review on the key components involved in altering dose efficacy and toxicity. Biochemistry and Biophysics Reports, 14, 125–132. 10.1016/j.bbrep.2018.04.008
  • Juengel, E., Thomas, A., Rutz, J., Makarevic, J., Tsaur, I., Nelson, K., Haferkamp, A., & Blaheta, R. A. (2016). Amygdalin inhibits the growth of renal cell carcinoma cells in vitro. International Journal of Molecular Medicine, 37(2), 526–532. 10.3892/ijmm.2015.2439
  • Knockaert, M., Greengard, P., & Meijer, L. (2002). Pharmacological inhibitors of cyclin-dependent kinases. Trends in Pharmacological Sciences, 23(9), 417–425. 10.1016/S0165-6147(02)02071-0
  • Konstantinidis, A. K., Radhakrishnan, R., Gu, F., Rao, R. N., & Yeh, W.-K. (1998). Purification, characterization, and kinetic mechanism of cyclin D1· CDK4, a major target for cell cycle regulation. Journal of Biological Chemistry, 273(41), 26506–26515. 10.1074/jbc.273.41.26506
  • Kumar, N., Gupta, S., Chand Yadav, T., Pruthi, V., Kumar Varadwaj, P., & Goel, N. (2019). Extrapolation of phenolic compounds as multi-target agents against cancer and inflammation. Journal of Biomolecular Structure and Dynamics, 37(9), 2355–2369. 10.1080/07391102.2018.1481457
  • Lapenna, S., & Giordano, A. (2009). Cell cycle kinases as therapeutic targets for cancer. Nature Reviews Drug Discovery, 8(7), 547–566. 10.1038/nrd2907
  • Lee, H. M., & Moon, A. (2016). Amygdalin regulates apoptosis and adhesion in Hs578T triple-negative breast cancer cells. Biomolecules & Therapeutics, 24(1), 62. 10.4062/biomolther.2015.172
  • Lim, S., & Kaldis, P. (2013). Cdks, cyclins and CKIs: Roles beyond cell cycle regulation. Development, 140(15), 3079–3093. 10.1242/dev.091744
  • Makarević, J., Rutz, J., Juengel, E., Kaulfuss, S., Reiter, M., Tsaur, I., Bartsch, G., Haferkamp, A., & Blaheta, R. A. (2014). Amygdalin blocks bladder cancer cell growth in vitro by diminishing cyclin A and cdk2. PLoS One, 9(8), e105590. 10.1371/journal.pone.0105590
  • Makarević, J., Rutz, J., Juengel, E., Kaulfuss, S., Tsaur, I., Nelson, K., Pfitzenmaier, J., Haferkamp, A., & Blaheta, R. A. (2014). Amygdalin influences bladder cancer cell adhesion and invasion in vitro. PLoS One, 9(10), e110244. 10.1371/journal.pone.0110244
  • Makarević, J., Tsaur, I., Juengel, E., Borgmann, H., Nelson, K., Thomas, C., Bartsch, G., Haferkamp, A., & Blaheta, R. A. (2016). Amygdalin delays cell cycle progression and blocks growth of prostate cancer cells in vitro. Life Sciences, 147, 137–142. 10.1016/j.lfs.2016.01.039
  • Malumbres, M., & Barbacid, M. (2005). Mammalian cyclin-dependent kinases. Trends in Biochemical Sciences, 30(11), 630–641. 10.1016/j.tibs.2005.09.005
  • Malumbres, M., & Barbacid, M. (2009). Cell cycle, CDKs and cancer: A changing paradigm. Nature Reviews Cancer, 9(3), 153–166. 10.1038/nrc2602
  • Manning, G., Whyte, D. B., Martinez, R., Hunter, T., & Sudarsanam, S. (2002). The protein kinase complement of the human genome. Science, 298(5600), 1912–1934. 10.1126/science.1075762
  • Mitra, A., Biswas, R., Bagchi, A., & Ghosh, R. (2019). Insight into the binding of a synthetic nitro-flavone derivative with human poly-ADP ribose polymerase 1. International Journal of Biological Macromolecules, 141, 444–459. 10.1016/j.ijbiomac.2019.08.242
  • Moertel, C. G., Ames, M. M., Kovach, J. S., Moyer, T. P., Rubin, J. R., & Tinker, J. H. (1981). A pharmacologic and toxicological study of amygdalin. JAMA: The Journal of the American Medical Association, 245(6), 591–594. 10.1001/jama.1981.03310310033018
  • Morgan, D. O. (1997). Cyclin-dependent kinases: Engines, clocks, and microprocessors. Annual Review of Cell and Developmental Biology, 13(1), 261–291. 10.1146/annurev.cellbio.13.1.261
  • Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., & Olson, A. J. (2009). AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of Computational Chemistry, 30(16), 2785–2791. 10.1002/jcc.21256
  • Obaya, A., & Sedivy, J. M. (2002). Regulation of cyclin-Cdk activity in mammalian cells. Cellular and Molecular Life Sciences: CMLS, 59(1), 126–142. 10.1007/s00018-002-8410-1
  • Pandey, R. K., Kumbhar, B. V., Sundar, S., Kunwar, A., & Prajapati, V. K. (2017). Structure-based virtual screening, molecular docking, ADMET and molecular simulations to develop benzoxaborole analogs as potential inhibitor against Leishmania donovani trypanothione reductase. Journal of Receptors and Signal Transduction, 37(1), 60–70. 10.3109/10799893.2016.1171344
  • Park, H.-J., Yoon, S.-H., Han, L.-S., Zheng, L.-T., Jung, K.-H., Uhm, Y.-K., … Yim, S.-V. (2005). Amygdalin inhibits genes related to cell cycle in SNU-C4 human colon cancer cells. World Journal of Gastroenterology: WJG, 11(33), 5156.
  • Peters, J.-M. (2006). The anaphase promoting complex/cyclosome: A machine designed to destroy. Nature Reviews Molecular Cell Biology, 7(9), 644–656. 10.1038/nrm1988
  • Pines, J., & Hunter, T. (1989). Isolation of a human cyclin cDNA: Evidence for cyclin mRNA and protein regulation in the cell cycle and for interaction with p34cdc2. Cell, 58(5), 833–846. 10.1016/0092-8674(89)90936-7
  • Qian, L., Xie, B., Wang, Y., & Qian, J. (2015). Amygdalin-mediated inhibition of non-small cell lung cancer cell invasion in vitro. International Journal of Clinical and Experimental Pathology, 8(5), 5363–5370.
  • Raghavendra, N. M., Pingili, D., Kadasi, S., Mettu, A., & Prasad, S. (2018). Dual or multi-targeting inhibitors: The next generation anticancer agents. European Journal of Medicinal Chemistry, 143, 1277–1300. 10.1016/j.ejmech.2017.10.021
  • Ravindranath, P. A., Forli, S., Goodsell, D. S., Olson, A. J., & Sanner, M. F. (2015). AutoDockFR: Advances in protein-ligand docking with explicitly specified binding site flexibility. PLoS Computational Biology, 11(12), e1004586. 10.1371/journal.pcbi.1004586
  • Sathishkumar, N., Sathiyamoorthy, S., Ramya, M., Yang, D.-U., Lee, H. N., & Yang, D.-C. (2012). Molecular docking studies of anti-apoptotic BCL-2, BCL-XL, and MCL-1 proteins with ginsenosides from Panax ginseng. Journal of Enzyme Inhibition and Medicinal Chemistry, 27(5), 685–692. 10.3109/14756366.2011.608663
  • Satyanarayana, A., & Kaldis, P. (2009). Mammalian cell-cycle regulation: Several Cdks, numerous cyclins and diverse compensatory mechanisms. Oncogene, 28(33), 2925–2939. 10.1038/onc.2009.170
  • Senderowicz, A. M. (2003). Small-molecule cyclin-dependent kinase modulators. Oncogene, 22(42), 6609–6620. 10.1038/sj.onc.1206954
  • Shi, H., & Zhang, R. (2009). Expression and significance of P53, P21WAF1 and CDK1 proteins in epithelial ovarian cancer. Chinese Journal of Cancer, 28(8), 882–885. 10.5732/cjc.008.10417
  • Shukla, R., Munjal, N. S., & Singh, T. R. (2019). Identification of novel small molecules against GSK3β for Alzheimer’s disease using chemoinformatics approach. Journal of Molecular Graphics and Modelling, 91, 91–104. 10.1016/j.jmgm.2019.06.008
  • Song, Z., & Xu, X. (2014). Advanced research on anti-tumor effects of amygdalin. Journal of Cancer Research and Therapeutics, 10(5), 3. 10.4103/0973-1482.139743
  • Vasanthakumari, D., Vadakkethil Lalithabhai, P., & Kanthimathi Bahuleyan, M. (2019). An in silico approach to discover the best molecular modeling strategy for designing novel CDK4 inhibitors. Chemical Biology & Drug Design, 93(4), 556–569. 10.1111/cbdd.13452
  • Wang, H., Dommert, F., & Holm, C. (2010). Optimizing working parameters of the smooth particle mesh Ewald algorithm in terms of accuracy and efficiency. The Journal of Chemical Physics, 133(3), 034117. 10.1063/1.3446812
  • Zhang, C., Elkahloun, A. G., Robertson, M., Gills, J. J., Tsurutani, J., Shih, J. H., Fukuoka, J., Hollander, M. C., Harris, C. C., Travis, W. D., Jen, J., & Dennis, P. A. (2011). Loss of cytoplasmic CDK1 predicts poor survival in human lung cancer and confers chemotherapeutic resistance. PLoS One, 6(8), e23849. 10.1371/journal.pone.0023849
  • Zoete, V., Cuendet, M. A., Grosdidier, A., & Michielin, O. (2011). SwissParam: A fast force field generation tool for small organic molecules. Journal of Computational Chemistry, 32(11), 2359–2368. 10.1002/jcc.21816

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