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Research Article

Spectroscopic insights with molecular docking and molecular dynamic simulation studies of anticancer drug 5-Fluorouracil targeting human pyruvate kinase m2

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Received 13 Oct 2023, Accepted 27 Jan 2024, Published online: 12 Feb 2024

References

  • Abraham, M. J., Murtola, T., Schulz, R., Páll, S., Smith, J. C., Hess, B., & Lindah, E. (2015). Gromacs: High performance molecular simulations through multi-level parallelism from laptops to supercomputers. SoftwareX, 1-2, 19–25. https://doi.org/10.1016/j.softx.2015.06.001
  • Albrecht, C. (2008). Joseph R. Lakowicz: Principles of fluorescence spectroscopy, 3rd Edition. Analytical and Bioanalytical Chemistry, 390(5), 1223–1224. https://doi.org/10.1007/s00216-007-1822-x
  • Amir, M., Mohammad, T., Prasad, K., Hasan, G. M., Kumar, V., Dohare, R., Islam, A., Ahmad, F., & Imtaiyaz Hassan, M. (2020). Virtual high-throughput screening of natural compounds in-search of potential inhibitors for protection of telomeres 1 (POT1). Journal of Biomolecular Structure & Dynamics, 38(15), 4625–4634. https://doi.org/10.1080/07391102.2019.1682052
  • Anand, U., Jash, C., Boddepalli, R. K., Shrivastava, A., & Mukherjee, S. (2011). Exploring the mechanism of fluorescence quenching in proteins induced by tetracycline. The Journal of Physical Chemistry. B, 115(19), 6312–6320. https://doi.org/10.1021/jp2008978
  • Azoitei, N., Becher, A., Steinestel, K., Rouhi, A., Diepold, K., Genze, F., Simmet, T., & Seufferlein, T. (2016). PKM2 promotes tumor angiogenesis by regulating HIF-1aα through NF-κB activation. Molecular Cancer, 15(3),1-15. https://doi.org/10.1186/s12943-015-0490-2
  • Behera, B. K., Parhi, J., Dehury, B., Rout, A. K., Khatei, A., Devi, A. L., & Mandal, S. C. (2022). Molecular characterization and structural dynamics of Aquaporin1 from walking catfish in lipid bilayers. International Journal of Biological Macromolecules, 196, 86–97. https://doi.org/10.1016/j.ijbiomac.2021.12.014
  • Bi, S., Yan, L., Sun, Y., & Zhang, H. (2011). Investigation of ketoprofen binding to human serum albumin by spectral methods. Spectrochimica Acta. Part A, Molecular and Biomolecular Spectroscopy, 78(1), 410–414. https://doi.org/10.1016/j.saa.2010.11.002
  • Chen, X., Chen, S., & Yu, D. (2020). Protein kinase function of pyruvate kinase M2 and cancer. Cancer Cell International, 20(523),1-11. https://doi.org/10.1186/s12935-020-01612-1
  • Chi, Z., & Liu, R. (2011). Phenotypic characterization of the binding of tetracycline to human serum albumin. Biomacromolecules, 12(1), 203–209. https://doi.org/10.1021/bm1011568
  • David, C. C., & Jacobs, D. J. (2014). Principal component analysis: A method for determining the essential dynamics of proteins. Methods in Molecular Biology (Clifton, N.J.), 1084, 193–226. https://doi.org/10.1007/978-1-62703-658-0_11
  • Dehury, B., Behera, S. K., & Mahapatra, N. (2017). Structural dynamics of Casein Kinase I (CKI) from malarial parasite Plasmodium falciparum (Isolate 3D7): Insights from theoretical modelling and molecular simulations. Journal of Molecular Graphics & Modelling, 71, 154–166. https://doi.org/10.1016/j.jmgm.2016.11.012
  • Dehury, B., & Kepp, K. P. (2021). Membrane dynamics of γ-secretase with the anterior pharynx-defective 1B subunit. Journal of Cellular Biochemistry, 122(1), 69–85. https://doi.org/10.1002/jcb.29832
  • Dehury, B., Patra, M. C., Maharana, J., Sahu, J., Sen, P., Modi, M. K., Choudhury, M. D., & Barooah, M. (2014). Structure-based computational study of two disease resistance gene homologues (Hm1 and Hm2) in maize (Zea mays L.) with implications in plant-pathogen. PloS One, 9(5), e97852. https://doi.org/10.1371/journal.pone.0097852
  • Dehury, B., Sahu, M., Patra, M. C., Sarma, K., Sahu, J., Sen, P., Modi, M. K., Choudhury, M. D., & Barooah, M. (2013). Insights into the structure-function relationship of disease resistance protein HCTR in maize (Zea mays L.): A computational structural biology approach. Journal of Molecular Graphics & Modelling, 45, 50–64. https://doi.org/10.1016/j.jmgm.2013.08.011
  • Dehury, B., Tang, N., Blundell, T. L. T. L., & Kepp, K. P. K. P. (2019). Structure and dynamics of γ-secretase with presenilin 2 compared to presenilin 1. RSC Advances, 9(36), 20901–20916. https://doi.org/10.1039/c9ra02623a
  • Dehury, B., Tang, N., Mehra, R., Blundell, T. L., & Kepp, K. P. (2020). Side-by-side comparison of Notch- And C83 binding to γ-secretase in a complete membrane model at physiological temperature. RSC Advances, 10(52), 31215–31232. https://doi.org/10.1039/d0ra04683c
  • Dey, S., Rout, M., Pati, S., Singh, M. K., Dehury, B., & Subudhi, E. (2023). All-atoms molecular dynamics study to screen potent efflux pump inhibitors against KpnE protein of Klebsiella pneumoniae. Journal of Biomolecular Structure & Dynamics,22,1–15. https://doi.org/10.1080/07391102.2023.2214232
  • Dufour, C., & Dangles, O. (2005). Flavonoid-serum albumin complexation: Determination of binding constants and binding sites by fluorescence spectroscopy. Biochimica et Biophysica Acta, 1721(1-3), 164–173. https://doi.org/10.1016/j.bbagen.2004.10.013
  • Garg, A., Mark Manidhar, D., Gokara, M., Malleda, C., Suresh Reddy, C., & Subramanyam, R. (2013). Elucidation of the Binding Mechanism of Coumarin Derivatives with Human Serum Albumin. PloS One, 8(5), e63805. https://doi.org/10.1371/journal.pone.0063805
  • Girdhar, K., Dehury, B., Kumar Singh, M., Daniel, V. P., Choubey, A., Dogra, S., Kumar, S., & Mondal, P. (2019). Novel insights into the dynamics behavior of glucagon-like peptide-1 receptor with its small molecule agonists. Journal of Biomolecular Structure & Dynamics, 37(15), 3976–3986. https://doi.org/10.1080/07391102.2018.1532818
  • Hess, B., Bekker, H., Berendsen, H. J. C., & Fraaije, J. G. E. M. (1997). LINCS: A linear constraint solver for molecular simulations. Journal of Computational Chemistry, 18(12), 1463–1472. https://doi.org/10.1002/(SICI)1096-987X(199709)18:12<1463::AID-JCC4>3.0.CO;2-H
  • Hu, Y. J., Liu, Y., & Xiao, X. H. (2009). Investigation of the interaction between Berberine and human serum albumin. Biomacromolecules, 10(3), 517–521. https://doi.org/10.1021/bm801120k
  • Hu, Y. J., Ou-Yang, Y., Dai, C. M., Liu, Y., & Xiao, X. H. (2010). Binding of berberine to bovine serum albumin: Spectroscopic approach. Molecular Biology Reports, 37(8), 3827–3832. https://doi.org/10.1007/s11033-010-0038-x
  • Huang, J., Rauscher, S., Nawrocki, G., Ran, T., Feig, M., De Groot, B. L., Grubmüller, H., & MacKerell, A. D. (2016). CHARMM36m: An improved force field for folded and intrinsically disordered proteins. Nature Methods, 14(1), 71–73. https://doi.org/10.1038/nmeth.4067
  • Humphrey, W., Dalke, A., & Schulten, K. (1996). VMD: Visual molecular dynamics. Journal of Molecular Graphics, 14(1), 33–38. https://doi.org/10.1016/0263-7855(96)00018-5
  • Israelsen, W. J., Dayton, T. L., Davidson, S. M., Fiske, B. P., Hosios, A. M., Bellinger, G., Li, J., Yu, Y., Sasaki, M., Horner, J. W., Burga, L. N., Xie, J., Jurczak, M. J., DePinho, R. A., Clish, C. B., Jacks, T., Kibbey, R. G., Wulf, G. M., Di Vizio, D., … Vander Heiden, M. G. (2013). XPKM2 isoform-specific deletion reveals a differential requirement for pyruvate kinase in tumor cells. Cell, 155(2), 397–409. https://doi.org/10.1016/j.cell.2013.09.025
  • Jha, Y., Dehury, B., Kumar, S. P. J., Chaurasia, A., Singh, U. B., Yadav, M. K., Angadi, U. B., Ranjan, R., Tripathy, M., Subramanian, R. B., Kumar, S., & Simal-Gandara, J. (2022). Delineation of molecular interactions of plant growth promoting bacteria induced β-1,3-glucanases and guanosine triphosphate ligand for antifungal response in rice: A molecular dynamics approach. Molecular Biology Reports, 49(4), 2579–2589. https://doi.org/10.1007/s11033-021-07059-5
  • Lehrer, S. S. (1971). Solute perturbation of protein fluorescence. the quenching of the tryptophyl fluorescence of model compounds and of lysozyme by iodide ion. Biochemistry, 10(17), 3254–3263. https://doi.org/10.1021/bi00793a015
  • Liu, W.-R., Tian, M.-X., Yang, L.-X., Lin, Y.-L., Jin, L., Ding, Z.-B., Shen, Y.-H., Peng, Y.-F., Gao, D.-M., Zhou, J., Qiu, S.-J., Dai, Z., He, R., Fan, J., & Shi, Y.-H. (2015). PKM2 promotes metastasis by recruiting myeloid-derived suppressor cells and indicates poor prognosis for hepatocellular carcinoma. Oncotarget, 6(2), 846–861. https://doi.org/10.18632/oncotarget.2749
  • Longley, D. B., Latif, T., Boyer, J., Allen, W. L., Maxwell, P. J., & Johnston, P. G. (2003). The interaction of thymidylate synthase expression with p53-regulated signaling pathways in tumor cells. Seminars in Oncology, 30(3 Suppl 6), 3–9. https://doi.org/10.1016/S0093-7754(03)70019-0
  • Luan, W., Wang, Y., Chen, X., Shi, Y., Wang, J., Zhang, J., Qian, J., Li, R., Tao, T., Wei, W., Hu, Q., Liu, N., & You, Y. (2015). PKM2 promotes glucose metabolism and cell growth in gliomas through a mechanism involving a let-7a/c-Myc/hnRNPA1 feedback loop. Oncotarget, 6(15), 13006–13018. https://doi.org/10.18632/oncotarget.3514
  • Mazurek, S. (2007). Pyruvate kinase type M2: A key regulator within the tumour metabolome and a tool for metabolic profiling of tumours. In Ernst Schering Foundation Symposium Proceedings, 4, 99–124. https://doi.org/10.1007/2789_2008_091
  • Mazurek, S. (2011). Pyruvate kinase type M2: A key regulator of the metabolic budget system in tumor cells. The International Journal of Biochemistry & Cell Biology, 43(7), 969–980. https://doi.org/10.1016/j.biocel.2010.02.005
  • Morris, G. M., Ruth, H., Lindstrom, W., Sanner, M. F., Belew, R. K., Goodsell, D. S., & Olson, A. J. (2009). Software news and updates AutoDock4 and AutoDockTools4: Automated docking with selective receptor flexibility. Journal of Computational Chemistry, 30(16), 2785–2791. https://doi.org/10.1002/jcc.21256
  • Murphy, C. B., Zhang, Y., Troxler, T., Ferry, V., Martin, J. J., & Jones, W. E. (2004). Probing Förster and Dexter energy-transfer mechanisms in fluorescent conjugated polymer chemosensors. The Journal of Physical Chemistry B, 108(5), 1537–1543. https://doi.org/10.1021/jp0301406
  • Olsson, M. H. M., SØndergaard, C. R., Rostkowski, M., & Jensen, J. H. (2011). PROPKA3: Consistent treatment of internal and surface residues in empirical p K a predictions. Journal of Chemical Theory and Computation, 7(2), 525–537. https://doi.org/10.1021/ct100578z
  • Pan, X., Qin, P., Liu, R., & Wang, J. (2011). Characterizing the interaction between tartrazine and two serum albumins by a hybrid spectroscopic approach. Journal of Agricultural and Food Chemistry, 59(12), 6650–6656. https://doi.org/10.1021/jf200907x
  • Pardini, B., Kumar, R., Naccarati, A., Novotny, J., Prasad, R. B., Forsti, A., Hemminki, K., Vodicka, P., & Lorenzo Bermejo, J. (2011). 5-Fluorouracil-based chemotherapy for colorectal cancer and MTHFR/MTRR genotypes. In. British Journal of Clinical Pharmacology, 72(1), 162–163. https://doi.org/10.1111/j.1365-2125.2010.03892.x
  • Patra, M. C., Maharana, J., Dehury, B., & De, S. (2014). Computational insights into the binding mechanism of antagonists with neuropeptide B/W receptor 1. Molecular bioSystems, 10(8), 2236–2246. https://doi.org/10.1039/c4mb00214h
  • Pattanayak, B. S., Dehury, B., Priyadarshinee, M., Jha, S., Beuria, T. K., Soren, D., & Mallick, B. C. (2021). Kanamycin-Mediated Conformational Dynamics of Escherichia coli Outer Membrane Protein TolC. Frontiers in Molecular Biosciences, 8, 636286–636301. https://doi.org/10.3389/fmolb.2021.636286
  • Ponce-Cusi, R., & Calaf, G. M. (2016). Apoptotic activity of 5-fluorouracil in breast cancer cells transformed by low doses of ionizing α-particle radiation. International Journal of Oncology, 48(2), 774–782. https://doi.org/10.3892/ijo.2015.3298
  • Rehman, M. T., Shamsi, H., & Khan, A. U. (2014). Insight into the binding mechanism of imipenem to human serum albumin by spectroscopic and computational approaches. Molecular Pharmaceutics, 11(6), 1785–1797. https://doi.org/10.1021/mp500116c
  • Ross, P. D., & Subramanian, S. (1981). Thermodynamics of proteins association reactions: forces contributing to stability. Biochemistry, 20(11), 3096–3102. https://doi.org/10.1021/bi00514a017
  • Rout, M., Dey, S., Mishra, S., Panda, S., Singh, M. K., Sinha, R., Dehury, B., & Pati, S. (2023). Machine learning and classical MD simulation to identify inhibitors against the P37 envelope protein of monkeypox virus. Journal of Biomolecular Structure & Dynamics, 23, 1–14. https://doi.org/10.1080/07391102.2023.2216290
  • Rout, M., Mishra, S., Dey, S., Singh, M. K., Dehury, B., & Pati, S. (2023). Exploiting the potential of natural polyphenols as antivirals against monkeypox envelope protein F13 using machine learning and all-atoms MD simulations. Computers in Biology and Medicine, 162, 107116. https://doi.org/10.1016/j.compbiomed.2023.107116
  • Shang, L., Wang, Y., Jiang, J., & Dong, S. (2007). PH-dependent protein conformational changes in albumin:Gold nanoparticle bioconjugates: A spectroscopic study. Langmuir: The ACS Journal of Surfaces and Colloids, 23(5), 2714–2721. https://doi.org/10.1021/la062064e
  • Shang, S., Liu, Q., Gao, J., Zhu, Y., Liu, J., Wang, K., Shao, W., & Zhang, S. (2014). Insights into In Vitro Binding of Parecoxib to Human Serum Albumin by Spectroscopic Methods. Journal of Biochemical and Molecular Toxicology, 28(10), 433–441. https://doi.org/10.1002/jbt.21582
  • Thoppil, A. A., Choudhary, S., & Kishore, N. (2016). Competitive binding of anticancer drugs 5-fluorouracil and cyclophosphamide with serum albumin: Calorimetric insights. Biochimica et Biophysica Acta, 1860(5), 917–929. https://doi.org/10.1016/j.bbagen.2016.01.026
  • Trott, O., & Olson, A. J. (2009). AutoDock Vina: Improving the speed and accuracy of docking with a new scoring function, efficient optimization, and multithreading. Journal of Computational Chemistry, 31(2), 455–461. https://doi.org/10.1002/jcc.21334
  • Valeur, B. (2012). Molecular fluorescence: Principles and applications. Print ISBN:9783527328376 |Online ISBN:9783527650002 | https://doi.org/10.1002/9783527650002, Copyright © 2012 Wiley‐VCH Verlag GmbH & Co. KGaA.
  • Vanommeslaeghe, K., Hatcher, E., Acharya, C., Kundu, S., Zhong, S., Shim, J., Darian, E., Guvench, O., Lopes, P., Vorobyov, I., & Mackerell, A. D. (2010). CHARMM general force field: A force field for drug-like molecules compatible with the CHARMM all-atom additive biological force fields. Journal of Computational Chemistry, 31(4), 671–690. https://doi.org/10.1002/jcc.21367
  • Ware, W. R. (1962). Oxygen quenching of fluorescence in solution: An experimental study of the diffusion process. The Journal of Physical Chemistry, 66(3), 455–458. https://doi.org/10.1021/j100809a020
  • Watt, R. M., & Voss, E. W. (1979). Solvent perturbation of the fluorescence of fluorescein bound to specific antibody. Fluorescence quenching of the bound fluorophore by iodide. The Journal of Biological Chemistry, 254(5), 1684–1690. https://doi.org/10.1016/s0021-9258(17)37827-4
  • Wilson, C. J., & Copeland, R. A. (1997). Spectroscopic characterization of arrestin interactions with competitive ligands: Study of heparin and phytic acid binding. Journal of Protein Chemistry, 16(8), 755–763. https://doi.org/10.1023/a:1026311832660
  • Wu, S., & Le, H. (2013). Dual roles of PKM2 in cancer metabolism. Acta Biochimica et Biophysica Sinica, 45(1), 27–35. https://doi.org/10.1093/abbs/gms106
  • Wyatt, M. D., & Wilson, D. M. (2009). Participation of DNA repair in the response to 5-fluorouracil. In. Cellular and Molecular Life Sciences: CMLS, 66(5), 788–799. https://doi.org/10.1007/s00018-008-8557-5
  • Xiao, H., Zhang, L., Chen, Y., Zhou, C., Wang, X., Wang, D., & Liu, Z. (2020). PKM2 promotes breast cancer progression by regulating epithelial mesenchymal transition. Analytical Cellular Pathology (Amsterdam), 2020, 8396023. https://doi.org/10.1155/2020/8396023
  • Xiao, Q., Huang, S., Liu, Y., Tian, F. F., & Zhu, J. C. (2009). Thermodynamics, conformation and active sites of the binding of Zn-Nd hetero-bimetallic schiff base to bovine serum albumin. Journal of Fluorescence, 19(2), 317–326. https://doi.org/10.1007/s10895-008-0418-y
  • Xiao, Q., Huang, S., Qi, Z. D., Zhou, B., He, Z. K., & Liu, Y. (2008). Conformation, thermodynamics and stoichiometry of HSA adsorbed to colloidal CdSe/ZnS quantum dots. Biochimica et Biophysica Acta, 1784(7-8), 1020–1027. https://doi.org/10.1016/j.bbapap.2008.03.018
  • Yang, C. Y., Liu, Y., Zheng, D., Zhu, J. C., & Dai, J. (2007). Luminescence of aniline blue in hydrophobic cavity of BSA. Journal of Photochemistry and Photobiology A: Chemistry, 188(1), 51–55. https://doi.org/10.1016/j.jphotochem.2006.11.017
  • Yue, Y., Liu, J., Fan, J., & Yao, X. (2011). Binding studies of phloridzin with human serum albumin and its effect on the conformation of protein. Journal of Pharmaceutical and Biomedical Analysis, 56(2), 336–342. https://doi.org/10.1016/j.jpba.2011.05.018
  • Zaidi, N., Ajmal, M. R., Rabbani, G., Ahmad, E., & Khan, R. H. (2013). A comprehensive insight into binding of hippuric acid to human serum albumin: A study to uncover its impaired elimination through hemodialysis. PloS One, 8(8), e71422. https://doi.org/10.1371/journal.pone.0071422
  • Zhang, N., Yin, Y., Xu, S. J., & Chen, W. S. (2008). 5-Fluorouracil: Mechanisms of resistance and reversal strategies. In. Molecules (Basel, Switzerland), 13(8), 1551–1569. https://doi.org/10.3390/molecules13081551
  • Zhao, L., Liu, R., Zhao, X., Yang, B., Gao, C., Hao, X., & Wu, Y. (2009). New strategy for the evaluation of CdTe quantum dot toxicity targeted to bovine serum albumin. The Science of the Total Environment, 407(18), 5019–5023. https://doi.org/10.1016/j.scitotenv.2009.05.052
  • Zhao, X., Liu, R., Chi, Z., Teng, Y., & Qin, P. (2010). New insights into the behavior of bovine serum albumin adsorbed onto carbon nanotubes: Comprehensive spectroscopic studies. The Journal of Physical Chemistry B, 114(16), 5625–5631. https://doi.org/10.1021/jp100903x
  • Zhivkova, Z. D. (2015). Studies on drug-human serum albumin binding: The current state of the matter. Current Pharmaceutical Design, 21(14), 1817–1830. www.rcsb.org/pdb https://doi.org/10.2174/1381612821666150302113710

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