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Antioxidative Properties of Usnic Acid and Its Interaction with Tyrosyl-DNA Phosphodiesterase

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Computational Bioengineering and Bioinformatics (ICCB 2019)

Part of the book series: Learning and Analytics in Intelligent Systems ((LAIS,volume 11))

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Abstract

In this study are investigated antioxidative properties of usnic acid, as well as its interaction with tyrosyl-DNA phosphodiesterase 1 (TDP1). Antioxidative properties are estimated on the basis of the Density Functional Theory (DFT) calculations. For this propose, full optimization of parent molecule of usnic acid and corresponding radical cation, radicals and anions are done at M05-2X/6-311++G(d,p) level of theory. The CPCM solvation model was applied to approximate the influence of polar and non-polar solvent. Obtained results indicate single electron transfer followed by the proton transfer as thermodynamically the most unfavorable mechanism of antioxidant action. The lowest values are achieved for proton affinity, and that pointed out sequential proton loss electron transfer mechanism as dominant antioxidative mechanism. The second part of this study is the examination of the interaction between usnic acid and TDP1, which is an enzyme responsible for repairing the protein-DNA bond in the cells. In order to perform molecular docking simulation AutoDock 4.0 software is used. Analysis of obtained data specifies interactions with Asn162, Leu168, Gly182, Tyr167 and Ser485 as the most significant. Further, the molecular dynamic simulation is performed using NAMD software. It is noticed that similar interactions are obtained.

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References

  1. Halliwell, B., Gutteridge, J.M.C.: Free Radicals in Biology and Medicine, 3rd edn. Clarendon Press, Oxford (1999)

    Google Scholar 

  2. Halliwell, B.: Free radicals and other reactive species in disease. In: Encyclopedia of Life Sciences. Nature Publishing Group (2001)

    Google Scholar 

  3. Rose, R.C., Bode, A.M.: Biology of free radical scavengers: an evaluation of ascorbate. FASEB J. 7(12), 1135–1142 (1993)

    Article  Google Scholar 

  4. Galano, A.: Free radicals induced oxidative stress at a molecular level: the current status, challenges and perspectives of computational chemistry based protocols. J. Mex. Chem. Soc. 59(4), 231–262 (2015)

    Google Scholar 

  5. Reyim, M.: Adiljan; Abdulla, A. China Brew. 11, 122–124 (2010)

    Google Scholar 

  6. Ingolfsdottir, K.: Usnic acid. Phytochemistry 61(7), 729–736 (2002)

    Article  Google Scholar 

  7. Araújo, A.A.S., De Melo, M.G.D., Rabelo, T.K., Nunes, P.S., Santos, S.L., Serafini, M.R., Santos, M.R.V., Quintans-Júnior, L.J., Gelain, D.P.: Review of the biological properties and toxicity of usnic acid. Nat. Prod. Res. 29(23), 2167–2180 (2015)

    Article  Google Scholar 

  8. Guo, L., Shi, Q., Fang, J.L., Mei, N., Ali, A.A., Lewis, S.M., Leakey, J.E., Frankos, V.H.: Review of usnic acid and Usnea barbata toxicity. J. Environ. Sci. Health Part C 26(4), 317–338 (2008)

    Article  Google Scholar 

  9. Shrestha, G., St. Clair, L.L.: Lichens: a promising source of antibiotic and anticancer drugs. Phytochem. Rev. 12(1), 229–244 (2013)

    Article  Google Scholar 

  10. Mitrović, T., Stamenković, S., Cvetković, V., Tošić, S., Stanković, M., Radojević, I., Stefanović, O., Čomić, L., Đačić, D., Ćurčić, M., Marković, S.: Antioxidant, antimicrobial and antiproliferative activities of five lichen species. Int. J. Mol. Sci. 12(8), 5428–5448 (2011)

    Article  Google Scholar 

  11. Bačkorová, M., Bačkor, M., Mikeš, J., Jendželovský, R., Fedoročko, P.: Lichen secondary metabolites are responsible for induction of apoptosis in HT-29 and A2780 human cancer cell lines. Toxicol. In Vitro 26(3), 462–468 (2012)

    Article  Google Scholar 

  12. Álvarez-Diduk, R., Galano, A.: Adrenaline and noradrenaline: protectors against oxidative stress or molecular targets? J. Phys. Chem. B 119(8), 3479–3491 (2015)

    Article  Google Scholar 

  13. Petrović, Z.D., Đorović, J., Simijonović, D., Petrović, V.P., Marković, Z.: Experimental and theoretical study of antioxidative properties of some salicylaldehyde and vanillic Schiff bases. RSC Adv. 5(31), 24094–24100 (2015)

    Article  Google Scholar 

  14. Alberto, M.E., Russo, N., Grand, A., Galano, A.: A physicochemical examination of the free radical scavenging activity of Trolox: mechanism, kinetics and influence of the environment. Phys. Chem. Chem. Phys. 15(13), 4642–4650 (2013)

    Article  Google Scholar 

  15. Galano, A., Mazzone, G., Alvarez-Diduk, R., Marino, T., Alvarez-Idaboy, R., Russo, N.: Food antioxidants: chemical insights at the molecular level. Ann. Rev. Food Sci. Technol. 7, 335–352 (2016)

    Article  Google Scholar 

  16. Rimarčík, J., Lukeš, V., Klein, E., Ilčin, M.: Study of the solvent effect on the enthalpies of homolytic and heterolytic N-H bond cleavage in p-phenylenediamine and tetracyano-p-phenylenediamine. J. Mol. Struct. (Thoechem) 952(1–3), 25–30 (2010)

    Article  Google Scholar 

  17. Zhang, H.Y., Ji, H.F.: How vitamin E scavenges DPPH radicals in polar protic media. New J. Chem. 30(4), 503–504 (2006)

    Article  Google Scholar 

  18. Frisch, M.J., Trucks, G.W., Schlegel, H.B., Scuseria, G.E., Robb, M.A., Cheeseman, J.R., Zakrzewski, V.G., Montgomery, J.J., Stratmann, R.E., Burant, J.C., Dapprich, S., Millam, J.M., Daniels, A.D., Kudin, K.N., Strain, M.C., Farkas, O., Tomasi, J., Barone, V., Cossi, M., Cammi, R., Mennucci, B., Pomelli, C., Adamo, C., Clifford, S., Ochterski, J., Petersson, G.A., Ayala, P.Y., Cui, Q., Morokuma, K., Malick, A.D., Rabuck, K.D., Raghavachari, K., Foresman, J.B., Cioslowski, J., Ortiz, J.V., Baboul, A.G., Stefanov, B.B., Liu, G., Liashenko, A., Piskorz, P., Komaromi, I., Gomperts, R., Martin, R.L., Fox, D.J., Keith, T., Al-Laham, M.A., Peng, C.Y., Nanayakkara, A., Challacombe, M., Gill, P.M.W., Johnson, B., Chen, W., Wong, M.W., Andres, J.L., Gonzalez, C., Head-Gordon, M., Replogle, E.S., Pople, J.A.: Gaussian 09, Revision B.01. Gaussian Inc., Wallingford (2009)

    Google Scholar 

  19. Zhao, Y., Truhlar, D.G.: The M06 suite of density functionals for main group thermochemistry, thermochemical kinetics, noncovalent interactions, excited states, and transition elements: two new functionals and systematic testing of four M06-class functionals and 12 other functionals. Theoret. Chem. Acc. 120(1), 215–241 (2008)

    Article  Google Scholar 

  20. Marković, Z.S., Marković, J.M.D., Doličanin, Ć.B.: Mechanistic pathways for the reaction of quercetin with hydroperoxy radical. Theoret. Chem. Acc. 127(1–2), 69–80 (2010)

    Article  Google Scholar 

  21. Marković, Z., Milenković, D., Đorović, J., Marković, J.M.D., Stepanić, V., Lučić, B., Amić, D.: Free radical scavenging activity of morin 2′-O− phenoxide anion. Food Chem. 135(3), 2070–2077 (2012)

    Article  Google Scholar 

  22. Zavala-Oseguera, C., Alvarez-Idaboy, J.R., Merino, G., Galano, A.: OH radical gas phase reactions with aliphatic ethers: a variational transition State Theory Study. J. Phys. Chem. A 113(50), 13913–13920 (2009)

    Article  Google Scholar 

  23. Takano, Y., Houk, K.N.: Benchmarking the conductor-like polarizable continuum model (CPCM) for aqueous solvation free energies of neutral and ionic organic molecules. J. Chem. Theory Comput. 1(1), 70–77 (2005)

    Article  Google Scholar 

  24. Tošović, J., Marković, S., Milenković, D., Marković, Z.: Solvation enthalpies and Gibbs energies of the proton and electron – influence of solvation models. J. Serb. Soc. Comput. Mech. 10(2), 66–76 (2016)

    Article  Google Scholar 

  25. Morris, G.M., Huey, R., Lindstrom, W., Sanner, M.F., Belew, R.K., Goodsell, D.S., Olson, A.J.: AutoDock4 and AutoDockTools4: automated docking with selective receptor flexibility. J. Comput. Chem. 30(16), 2785–2791 (2009)

    Article  Google Scholar 

  26. Davies, D.R., Interthal, H., Champoux, J.J., Hol, W.G.: The crystal structure of human tyrosyl-DNA phosphodiesterase, TDP1. Structure 10(2), 237–248 (2002)

    Article  Google Scholar 

  27. Phillips, J.C., Braun, R., Wang, W., Gumbart, J., Tajkhorshid, E., Villa, E., Chipot, C., Skeel, R.D., Kale, L., Schulten, K.: Scalable molecular dynamics with NAMD. J. Comput. Chem. 26(16), 1781–1802 (2005)

    Article  Google Scholar 

  28. Galasso, V.: Probing the molecular and electronic structure of the lichen metabolite usnic acid: a DFT study. Chem. Phys. 374(1–3), 138–145 (2010)

    Article  Google Scholar 

  29. Hussein, M.A.: A convenient mechanism for the free radical scavenging activity of resveratrol. Int. J. Phytomedicine 3(4), 459–469 (2011)

    MathSciNet  Google Scholar 

  30. Knight, J.A.: Review: free radicals, antioxidants, and the immune system. Ann. Clin. Lab. Sci. 30(2), 145–158 (2000)

    Google Scholar 

  31. Cooper, G.M.: The development and causes of cancer. In: The Cell: A Molecular Approach, 2nd edn., Boston University, Sunderland, MA. Sinauer Associates (2000)

    Google Scholar 

  32. Takagi, M., Ueda, J.Y., Hwang, J.H., Hashimoto, J., Izumikawa, M., Murakami, H., Sekido, Y., Shin-ya, K.: Tyrosyl-DNA phosphodiesterase 1 inhibitor from an anamorphic fungus. J. Nat. Prod. 75(4), 764–767 (2012)

    Article  Google Scholar 

  33. Antony, S., Marchand, C., Stephen, A.G., Thibaut, L., Agama, K.K., Fisher, R.J., Pommier, Y.: Novel high-throughput electrochemiluminescent assay for identification of human tyrosyl-DNA phosphodiesterase (TDP1) inhibitors and characterization of furamidine (NSC 305831) as an inhibitor of TDP1. Nucleic Acids Res. 35(13), 4474–4484 (2007)

    Article  Google Scholar 

  34. Gushchina, V., Nilov, D.K., Zakharenko, A.L., Lavrik, O.I., Švedas, V.K.: Structure modeling of human tyrosyldna phosphodiesterase 1 and screening for its inhibitors. Acta Naturae 9(2(33)), 59–66 (2017)

    Article  Google Scholar 

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Acknowledgments

The authors acknowledge support of the Ministry of Education, Science and Technological Development of the Republic of Serbia (Grants no. 174028 and 172015).

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Authors and Affiliations

  1. Bioengineering Research and Development Center - BioIRC, 34000, Kragujevac, Republic of Serbia

    Jelena Đorović & Zoran Marković

  2. Department of Science, Institute for Information Technologies, University of Kragujevac, Jovana Cvijića bb, 34000, Kragujevac, Republic of Serbia

    Zoran Marković

Authors
  1. Jelena Đorović
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  2. Zoran Marković
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Correspondence to Jelena Đorović .

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Editors and Affiliations

  1. Faculty of Engineering, University of Kragujevac, Kragujevac, Serbia

    Nenad Filipovic

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Đorović, J., Marković, Z. (2020). Antioxidative Properties of Usnic Acid and Its Interaction with Tyrosyl-DNA Phosphodiesterase. In: Filipovic, N. (eds) Computational Bioengineering and Bioinformatics. ICCB 2019. Learning and Analytics in Intelligent Systems, vol 11. Springer, Cham. https://doi.org/10.1007/978-3-030-43658-2_8

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  • DOI: https://doi.org/10.1007/978-3-030-43658-2_8

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  • Publisher Name: Springer, Cham

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  • Online ISBN: 978-3-030-43658-2

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