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Research Articles

Understanding the mechanism of amygdalin’s multifunctional anti-cancer action using computational approach

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Pages 1600-1610 | Received 21 Dec 2019, Accepted 19 Feb 2020, Published online: 09 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. doi:10.1016/j.softx.2015.06.001
  • Anantram, A., Kundaikar, H., Degani, M., & Prabhu, A. (2019). Molecular dynamic simulations on an inhibitor of anti-apoptotic Bcl-2 proteins for insights into its interaction mechanism for anti-cancer activity. Journal of Biomolecular Structure and Dynamics, 37(12), 3109–3121. doi:10.1080/07391102.2018.1508371
  • Bellocchi, D., Macchiarulo, A., Costantino, G., & Pellicciari, R. (2005). Docking studies on PARP-1 inhibitors: Insights into the role of a binding pocket water molecule. Bioorganic & Medicinal Chemistry, 13(4), 1151–1157. doi:10.1016/j.bmc.2004.11.024
  • Bhatnagar, A., Mittal, S., & Garg, A. (2017). Laetrile: A wonder drug or farce. International Journal of Applied Dental Sciences, 3, 42–45.
  • Biovia, D. S. (2019). Discovery Studio modeling environment. San Diego: Dassault Systèmes BIOVIA, Discovery Studio, 2019; Dassault Systèmes, 2016.
  • 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. doi:10.1021/ct900549r
  • Chang, H.-K., Shin, M.-S., Yang, H.-Y., Lee, J.-W., Kim, Y.-S., Lee, M.-H., Kim, J., Kim, K.-H., & Kim, C.-J. (2006). Amygdalin induces apoptosis through regulation of Bax and Bcl-2 expressions in human DU145 and LNCaP prostate cancer cells. Biological & Pharmaceutical Bulletin, 29(8), 1597–1602. doi:10.1248/bpb.29.1597
  • Chen, Y., Ma, J., Wang, F., Hu, J., Cui, A., Wei, C., Yang, Q., & Li, F. (2013). Amygdalin induces apoptosis in human cervical cancer cell line HeLa cells. Immunopharmacology and Immunotoxicology, 35(1), 43–51. doi:10.3109/08923973.2012.738688
  • Croce, C. M., & Reed, J. C. (2016). Finally, an apoptosis-targeting therapeutic for cancer. Cancer Research, 76(20), 5914–5920. doi:10.1158/0008-5472.CAN-16-1248
  • Darden, T., York, D., & Pedersen, L. (1993). Particle mesh Ewald: An N⋅log(N) method for Ewald sums in large systems. The Journal of Chemical Physics, 98(12), 10089–10092. doi:10.1063/1.464397
  • De Vivo, M., Masetti, M., Bottegoni, G., & Cavalli, A. (2016). Role of molecular dynamics and related methods in drug discovery. Journal of Medicinal Chemistry, 59(9), 4035–4061. doi:10.1021/acs.jmedchem.5b01684
  • Diamantopoulos, P. T., Sofotasiou, M., Papadopoulou, V., Polonyfi, K., Iliakis, T., & Viniou, N.-A. (2014). PARP1-driven apoptosis in chronic lymphocytic leukemia. BioMed Research International, 2014, 1–6. doi:10.1155/2014/106713
  • Ding, J., Zhang, Z., Roberts, G. J., Falcone, M., Miao, Y., Shao, Y., Zhang, X. C., Andrews, D. W., & Lin, J. (2010). Bcl-2 and Bax interact via the BH1–3 groove-BH3 motif interface and a novel interface involving the BH4 motif. Journal of Biological Chemistry, 285(37), 28749–28763. doi:10.1074/jbc.M110.148361
  • Feinstein, W. P., & Brylinski, M. (2015). Calculating an optimal box size for ligand docking and virtual screening against experimental and predicted binding pockets. Journal of Cheminformatics, 7(1), 18. doi:10.1186/s13321-015-0067-5
  • Ferreira, L., dos Santos, R., Oliva, G., & Andricopulo, A. (2015). Molecular docking and structure-based drug design strategies. Molecules, 20(7), 13384–13421. doi:10.3390/molecules200713384
  • Frauenfelder, H., Sligar, S. G., & Wolynes, P. G. (1991). The energy landscapes and motions of proteins. Science, 254(5038), 1598–1603. doi:10.1126/science.1749933
  • Gaba, M., Punam, G., & Sarbjot, S. (2010). An overview on molecular docking. International Journal of Drug Development and Research, 2, 219–231.
  • 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(16), 4327–4337. doi:10.1080/07391102.2018.1546621
  • Jan, R., & Chaudhry, G-e-S. (2019). Understanding apoptosis and apoptotic pathways targeted cancer therapeutics. Advanced Pharmaceutical Bulletin, 9(2), 205–218. doi:10.15171/apb.2019.024
  • Juengel, E. V. A., 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. doi:10.3892/ijmm.2015.2439
  • 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. doi:10.1080/07391102.2018.1481457
  • Kumar, S. (1995). ICE-like proteases in apoptosis. Trends in Biochemical Sciences, 20(5), 198–202. doi:10.1016/S0968-0004(00)89007-6
  • Lee, H. M., & Moon, A. (2016). Amygdalin regulates apoptosis and adhesion in Hs578T triple-negative breast cancer cells. Biomolecules & Therapeutics, 24(1), 62. doi:10.4062/biomolther.2015.172
  • Liu, X., Zou, H., Slaughter, C., & Wang, X. (1997). DFF, a heterodimeric protein that functions downstream of caspase-3 to trigger DNA fragmentation during apoptosis. Cell, 89(2), 175–184. doi:10.1016/S0092-8674(00)80197-X
  • 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. doi: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. doi:10.1371/journal.pone.0110244
  • 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. doi:10.1016/j.ijbiomac.2019.08.242
  • Mohammad, R. M., Muqbil, I., Lowe, L., Yedjou, C., Hsu, H.-Y., Lin, L.-T., Siegelin, M. D., Fimognari, C., Kumar, N. B., Dou, Q. P., Yang, H., Samadi, A. K., Russo, G. L., Spagnuolo, C., Ray, S. K., Chakrabarti, M., Morre, J. D., Coley, H. M., Honoki, K., … Azmi, A. S. (2015). Broad targeting of resistance to apoptosis in cancer. Seminars in Cancer Biology, 35, S78–S103. doi:10.1016/j.semcancer.2015.03.001
  • Morris, G. M., Huey, R., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S. and Olson, A. J. (2009) Autodock4 and AutoDockTools4: automated docking with selective receptor flexiblity. Journal of Computational Chemistry, 30(16), 2785–2791. doi: 10.1002/jcc.21256.
  • O’Boyle, N. M., Banck, M., James, C. A., Morley, C., Vandermeersch, T., & Hutchison, G. R. (2011). Open Babel: An open chemical toolbox. Journal of Cheminformatics, 3(1), 33. doi:10.1186/1758-2946-3-33
  • 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. doi:10.3109/10799893.2016.1171344
  • Park, H.-J., Yoon, S.-H., Han, L.-S., Zheng, L.-T., Jung, K.-H., Uhm, Y.-K., Lee, J.-H., Jeong, J.-S., Joo, W.-S., Yim, S.-V., Chung, J.-H., & Hong, S.-P. (2005). Amygdalin inhibits genes related to cell cycle in SNU-C4 human colon cancer cells. World Journal of Gastroenterology, 11(33), 5156–5161. doi:10.3748/wjg.v11.i33.5156
  • Pfeffer, C., & Singh, A. (2018). Apoptosis: A target for anticancer therapy. International Journal of Molecular Sciences, 19(2), 448.
  • Piana, S., & Rothlisberger, U. (2004). Molecular dynamics simulations of structural changes during procaspase 3 activation. Proteins: Structure, Function, and Bioinformatics, 55(4), 932–941. doi:10.1002/prot.20046
  • Pinto, M., Perez, J. J., & Rubio-Martinez, J. (2004). Molecular dynamics study of peptide segments of the BH3 domain of the proapoptotic proteins Bak, Bax, Bid and Hrk bound to the Bcl-x L and Bcl-2 proteins. Journal of Computer-Aided Molecular Design, 18(1), 13–22. doi:10.1023/B:JCAM.0000022559.72848.1c
  • Porter, A. G., & Jänicke, R. U. (1999). Emerging roles of caspase-3 in apoptosis. Cell Death & Differentiation, 6(2), 99–104. doi:10.1038/sj.cdd.4400476
  • 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. doi: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. doi:10.1371/journal.pcbi.1004586
  • Samuel, S., Tumilasci, V. F., Oliere, S., Nguyên, T. L.-A., Shamy, A., Bell, J., & Hiscott, J. (2010). VSV oncolysis in combination with the BCL-2 inhibitor obatoclax overcomes apoptosis resistance in chronic lymphocytic leukemia. Molecular Therapy, 18(12), 2094–2103. doi:10.1038/mt.2010.188
  • 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. doi:10.3109/14756366.2011.608663
  • Shen, H., Sun, H., & Li, G. (2012). What is the role of motif D in the nucleotide incorporation catalyzed by the RNA-dependent RNA polymerase from poliovirus? PLoS Computational Biology, 8(12), e1002851. doi:10.1371/journal.pcbi.1002851
  • 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. doi:10.1016/j.jmgm.2019.06.008
  • Singh, A., Somvanshi, P., & Grover, A. (2019). Pyrazinamide drug resistance in RpsA mutant (Δ438A) of Mycobacterium tuberculosis: Dynamics of essential motions and free-energy landscape analysis. Journal of Cellular Biochemistry, 120(5), 7386–7402. doi:10.1002/jcb.28013
  • Soldani, C., & Scovassi, A. (2002). Poly(ADP-ribose) polymerase-1 cleavage during apoptosis: An update. Apoptosis: An International Journal on Programmed Cell Death, 7(4), 321–328. doi:10.1023/a:1016119328968
  • Song, Z., & Xu, X. (2014). Advanced research on anti-tumor effects of amygdalin. Journal of Cancer Research and Therapeutics, 10(5), 3. doi:10.4103/0973-1482.139743
  • Thornberry, N. A., Rano, T. A., Peterson, E. P., Rasper, D. M., Timkey, T., Garcia-Calvo, M., Houtzager, V. M., Nordstrom, P. A., Roy, S., Vaillancourt, J. P., Chapman, K. T., & Nicholson, D. W. (1997). A combinatorial approach defines specificities of members of the caspase family and granzyme B Functional relationships established for key mediators of apoptosis. Journal of Biological Chemistry, 272(29), 17907–17911. doi:10.1074/jbc.272.29.17907
  • Verma, S., Singh, A., & Mishra, A. (2015). Complex disruption effect of natural polyphenols on Bcl-2-Bax: Molecular dynamics simulation and essential dynamics study. Journal of Biomolecular Structure and Dynamics, 33(5), 1094–1106. doi:10.1080/07391102.2014.931823
  • Virág, L., & Szabó, C. (2002). The therapeutic potential of poly(ADP-ribose) polymerase inhibitors. Pharmacological Reviews, 54(3), 375–429. doi:10.1124/pr.54.3.375
  • Walters, J., Pop, C., Scott, F. L., Drag, M., Swartz, P., Mattos, C., Salvesen, G. S., & Clark, A. C. (2009). A constitutively active and uninhibitable caspase-3 zymogen efficiently induces apoptosis. Biochemical Journal, 424(3), 335–345. doi:10.1042/BJ20090825
  • Węsierska-Gądek, J., Gueorguieva, M., Wojciechowski, J., Tudzarova-Trajkovska, S. (2004). In vivo activated caspase‐3 cleaves PARP‐1 in rat liver after administration of the hepatocarcinogen N‐nitrosomorpholine (NNM) generating the 85 kDa fragment. Journal of Cellular Biochemistry, 93(4), 774–787. doi:10.1002/jcb.20181
  • Zhao, Q., Lan, T., Su, S., & Rao, Y. (2019). Induction of apoptosis in MDA-MB-231 breast cancer cells by a PARP1-targeting PROTAC small molecule. Chemical Communications, 55(3), 369–372. doi:10.1039/C8CC07813K
  • 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. doi:10.1002/jcc.21816

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