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Research Article

Computational investigation of impact of Pb(II) and Ni(II) ions on hUNG enzyme: insights from molecular dynamics simulations

, ORCID Icon, , ORCID Icon, &
Received 08 Jul 2023, Accepted 08 Jan 2024, Published online: 27 Jan 2024

References

  • Abraham, M. J., Hess, B., van der Spoel, D., & Lindahl, E. (2018). GROMACS user manual version 2018.
  • Balali-Mood, M., Naseri, K., Tahergorabi, Z., Khazdair, M. R., & Sadeghi, M. (2021). Toxic mechanisms of five heavy metals: mercury, lead, chromium, cadmium, and arsenic. Frontiers in Pharmacology, 12, 643972. https://doi.org/10.3389/fphar.2021.643972
  • Bao, H., He, W., & Chen, J. (2023). Exploring conformation changes of Janus kinase 2 pseudokinase mediated by mutations through Gaussian accelerated molecular dynamics and principal component analysis. Journal of Biomolecular Structure & Dynamics, 1–18. https://doi.org/10.1080/07391102.2023.2260486
  • Chen, J., Zeng, Q., Wang, W., Sun, H., & Hu, G. (2022). Decoding the identification mechanism of an SAM-III Riboswitch on ligands through multiple independent Gaussian-accelerated molecular dynamics simulations. Journal of Chemical Information and Modeling, 62(23), 6118–6132. https://doi.org/10.1021/ACS.JCIM.2C00961/SUPPL_FILE/CI2C00961_SI_003.PDF
  • Chung, J. H., Im, E. K., Park, H. Y., Kwon, J. H., Lee, S., Oh, J., Hwang, K. C., Lee, J. H., & Jang, Y. (2003). A novel uracil-DNA glycosylase family related to the helix-hairpin-helix DNA glycosylase superfamily. Nucleic Acids Research, 31(8), 2045–2055. https://doi.org/10.1093/nar/gkg319
  • Dalal, V., Dhankhar, P., Singh, V., Singh, V., Rakhaminov, G., Golemi-Kotra, D., & Kumar, P. (2021). Structure-based identification of potential drugs against FmtA of Staphylococcus aureus: virtual screening, molecular dynamics, MM-GBSA, and QM/MM. The Protein Journal, 40(2), 148–165. https://doi.org/10.1007/s10930-020-09953-6
  • Durham, E., Dorr, B., Woetzel, N., Staritzbichler, R., & Meiler, J. (2009). Solvent accessible surface area approximations for rapid and accurate protein structure prediction. Journal of Molecular Modeling, 15(9), 1093–1108. https://doi.org/10.1007/s00894-009-0454-9
  • Dushanan, R., Weerasinghe, S., Dhammike, P., & Senthilinithy, R. (2022). Cracking a cancer code histone deacetylation in epigenetic : The implication from molecular dynamics simulations on efficacy assessment of histone deacetylase inhibitors. Journal of Biomolecular Structure & Dynamics, 40(5), 2352–2368. https://doi.org/10.1080/07391102.2020.1838328
  • Dushanan, R., Weerasinghe, S., Dissanayake, D. P., & Senthilnithy, R. (2022). Driving the new generation histone deacetylase inhibitors in cancer therapy; manipulation of the histone abbreviation at the epigenetic level: An in-silico approach. Canadian Journal of Chemistry, 100(12), 880–890. https://doi.org/10.1139/cjc-2022-0056
  • Dushanan, R., Weerasinghe, S., Dissanayake, D. P., & Senthilnithy, R. (2022). Implication of Ab Initio, QM/MM and molecular dynamics calculations on the prediction of the therapeutic potential of some selected HDAC inhibitors. Molecular Simulation, 48(16), 1464–1475. https://doi.org/10.1080/08927022.2022.2097672
  • Dushanan, R., Weerasinghe, S., Dissanayake, D. P., & Senthilnithy, R. (2021). An in-silico approach to evaluate the inhibitory potency of selected hydroxamic acid derivatives on zinc-dependent histone deacetylase enzyme. Journal of Computational Biophysics and Chemistry, 20(06), 603–618. https://doi.org/10.1142/S2737416521500356
  • Dyson, H. J., Wright, P. E., & Scheraga, H. A. (2006). The role of hydrophobic interactions in initiation and propagation of protein folding. Proceedings of the National Academy of Sciences of the United States of America, 103(35), 13057–13061. https://doi.org/10.1073/PNAS.0605504103/ASSET/A63FAF4F-488D-48DB-A595-78DDBCDF592E/ASSETS/GRAPHIC/ZPQ0340632240005.JPEG
  • Ebrahimi, R., Ebrahimi, M., & Shakeri, M. (2023). Mitigating the adverse effects of lead and cadmium heavy metals-induced oxidative stress by phytogenic compounds in poultry. Poultry, 2(2), 235–251. https://doi.org/10.3390/poultry2020019
  • Gokey, T., Hang, B., & Guliaev, A. B. (2016). Cadmium(II) inhibition of human uracil-DNA glycosylase by catalytic water supplantation. Scientific Reports, 6(1), 39137. https://doi.org/10.1038/srep39137
  • Huang, J., & Mackerell, A. D. (2013). CHARMM36 all-atom additive protein force field: validation based on comparison to NMR data. Journal of Computational Chemistry, 34(25), 2135–2145. https://doi.org/10.1002/jcc.23354
  • 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
  • Izadi, S., & Onufriev, A. V. (2016). Accuracy limit of Rigid 3-point water models. The Journal of Chemical Physics, 145(7), 074501. https://doi.org/10.1063/1.4960175
  • Jaishankar, M., Tseten, T., Anbalagan, N., Mathew, B. B., & Beeregowda, K. N. (2014). Toxicity, mechanism and health effects of some heavy metals. Interdisciplinary Toxicology, 7(2), 60–72. https://doi.org/10.2478/intox-2014-0009
  • Kavli, B., Otterlei, M., Slupphaug, G., & Krokan, H. E. (2007). Uracil in DNA-general mutagen, but normal intermediate in acquired immunity. DNA Repair, 6(4), 505–516. https://doi.org/10.1016/j.dnarep.2006.10.014
  • Kuzmanic, A., & Zagrovic, B. (2010). Determination of ensemble-average pairwise root mean-square deviation from experimental B-factors. Biophysical Journal, 98(5), 861–871. https://doi.org/10.1016/J.BPJ.2009.11.011
  • Kwofie, S. K., Broni, E., Yunus, F. U., Nsoh, J., Adoboe, D., Miller, W. A., & Wilson, M. D. (2021). Molecular docking simulation studies identifies potential natural product derived-antiwolbachial compounds as filaricides against onchocerciasis. Biomedicines, 9(11), 1682. https://doi.org/10.3390/BIOMEDICINES9111682
  • Madeswaran, A., Umamaheswari, M., Asokkumar, K., Sivashanmugam, T., Subhadradevi, V., & Jagannath, P. (2011). In silico docking studies of aldose reductase inhibitory activity of commercially available flavonoids. J. Comput. Methods Mol. Des, 1(4), 65–72. https://doi.org/10.3329/bjp.v7i4.12314
  • Martínez, L. (2015). Automatic identification of mobile and rigid substructures in molecular dynamics simulations and fractional structural fluctuation analysis. PLoS One, 10(3), e0119264. https://doi.org/10.1371/journal.pone.0119264
  • McNeill, D. R., Narayana, A., Wong, H. K., & Wilson, D. M. (2004). Inhibition of ape1 nuclease activity by lead, iron, and cadmium. Environmental Health Perspectives, 112(7), 799–804. https://doi.org/10.1289/txg.7038
  • Mitra, S., Chakraborty, A. J., Tareq, A. M., Emran, T., Bin; Nainu, F., Khusro, A., Idris, A. M., Khandaker, M. U., Osman, H., Alhumaydhi, F. A., & Simal-Gandara, J. (2022). Impact of heavy metals on the environment and human health: novel therapeutic insights to counter the toxicity. Journal of King Saud University - Science, 34(3), 101865. https://doi.org/10.1016/j.jksus.2022.101865
  • Olinski, R., Jurgowiak, M., & Zaremba, T. (2010). Uracil in DNA-its biological significance. Mutation Research, 705(3), 239–245. https://doi.org/10.1016/j.mrrev.2010.08.001
  • Paligaspe, P., Weerasinghe, S., Dissanayake, D. P., & Senthilnithy, R. (2022). Impact of Cd(II) on the stability of human uracil DNA glycosylase enzyme; an implication of molecular dynamics trajectories on stability analysis. Journal of Biomolecular Structure & Dynamics, 40(24), 14027–14034. https://doi.org/10.1080/07391102.2021.1999329
  • Parthiban, G., Dushanan, R., Weerasinghe, S., Dissanayake, D., & Senthilnithy, R. (2022). Exploration of novel mono hydroxamic acid derivatives as inhibitors for histone deacetylase like protein (HDLP) by molecular dynamics studies. Indonesian Journal of Chemistry, 22(6), 1534–1552. https://doi.org/10.22146/ijc.74167
  • Paligaspe, P., Weerasinghe, S., Dissanayake, D. P., & Senthilnithy, R. (2021). Identify the effect of As(III) on the structural stability of monomeric PKM2 and its carcinogenicity: A molecular dynamics and QM/MM based approach. Journal of Molecular Structure, 1235. https://doi.org/10.1016/j.molstruc.2021.130257
  • Pearl, L. H. (2000). Structure and function in the uracil-DNA glycosylase superfamily. Mutation Research, 460(3-4), 165–181. https://doi.org/10.1016/S0921-8777(00)00025-2
  • Reva, B. A., Finkelstein, A. V., & Skolnick, J. (1998). What is the probability of a chance prediction of a protein structure with an RMSD of 6 A? Folding & Design, 3(2), 141–147. https://doi.org/10.1016/S1359-0278(98)00019-4
  • Rousseau, M. C., Parent, M. E., Nadon, L., Latreille, B., & Siemiatycki, J. (2007). Occupational exposure to lead compounds and risk of cancer among men: A population-based case-control study. American Journal of Epidemiology, 166(9), 1005–1014. https://doi.org/10.1093/AJE/KWM183
  • Schärer, O. D., & Jiricny, J. (2001). Recent progress in the biology, chemistry and structural biology of DNA glycosylases. BioEssays, 23(3), 270–281. https://doi.org/10.1002/1521-1878(200103)23:3<270::AID-BIES1037>3.0.CO;2-J
  • Schormann, N., Ricciardi, R., & Chattopadhyay, D. (2014). Uracil-DNA glycosylases - structural and functional perspectives on an essential family of DNA repair enzymes. Protein Science: A Publication of the Protein Society, 23(12), 1667–1685. https://doi.org/10.1002/pro.2554
  • Seeliger, D., & De Groot, B. L. (2010). Conformational transitions upon ligand binding: Holo-structure prediction from APO conformations. PLoS Computational Biology, 6(1), e1000634. https://doi.org/10.1371/JOURNAL.PCBI.1000634
  • Singh, R., Gautam, N., Mishra, A., & Gupta, R. (2011). Heavy metals and living systems: An overview. Indian Journal of Pharmacology, 43(3), 246. https://doi.org/10.4103/0253-7613.81505
  • Tchounwou, P. B., Yedjou, C. G., Patlolla, A. K., & Sutton, D. J. (2012). Heavy metal toxicity and the environment. Molecular and Environmental Toxicology, 101, 133–164. https://doi.org/10.1007/978-3-7643-8340-4_6
  • Wallace, A. C., Laskowski, R. A., Thornton, J. M., Wallace, A. C., Laskowski, R. A., & Thornton, J. M. (1995). LIGPLOT: A program to generate schematic diagrams of protein-ligand interactions. Protein Engineering, 8(2), 127–134. https://doi.org/10.1093/Protein/8.2.127
  • Wang, P., Guliaev, A. B., & Hang, B. (2006). Metal inhibition of human N-methylpurine-DNA glycosylase activity in base excision repair. Toxicology Letters, 166(3), 237–247. https://doi.org/10.1016/j.toxlet.2006.06.647
  • Weber, S. (2005). Light-driven enzymatic catalysis of DNA repair: A review of recent biophysical studies on photolyase. Biochimica et Biophysica Acta, 1707(1), 1–23. https://doi.org/10.1016/j.bbabio.2004.02.010
  • Won, Y. (2012). Force field for monovalent, divalent, and trivalent cations developed under the solvent boundary potential. The Journal of Physical Chemistry. A, 116(47), 11763–11767. https://doi.org/10.1021/jp309150r
  • Xu, Y., Wang, S., Hu, Q., Gao, S., Ma, X., Zhang, W., Shen, Y., Chen, F., Lai, L., & Pei, J. (2018). CavityPlus: a web server for protein cavity detection with pharmacophore modelling, allosteric site identification, and covalent ligand binding ability prediction. Nucleic Acids Research, 46(W1), W374–W379. https://doi.org/10.1093/nar/gky380

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